Wii Warm Up: Say goodnight to the bad guy
by David Hinkle 
{ Apr 22nd 2008 at 9:00AM }
For us gamers, boss fights are something to be cherished and savored, like a fine bottle of wine. Over the years, we've had some pretty memorable boss battles. This, obviously, got us thinking about you all and what memorable boss encounters you might be able to recall.
So tell us about your favorite boss battles, either of recent memory (like, say, taking on Ganon at the end of Twilight Princess) or your favorites of all time (uh, the secret ending of No More Heroes, anyone?). Who did you enjoy defeating? Who did you hate fighting?
Reader Comments (Page 1 of 2)
Mike D @ Apr 22nd 2008 9:12AM
I just beat RE:4 wii last night, and I was pretty disappointed by the final boss. He was fairly straightforward. I gotta agree on the TP battle (all 3 of them), that was epic.
Bowser in Mario Galaxy was pathetically easy.
The only other battle that really sticks out in my mind is Mother Brain from the first Metroid game.
Roto13 @ Apr 22nd 2008 9:30AM
I considered it to be four. :P
coleduke @ Apr 22nd 2008 9:36AM
+1 on Mother Brain. That's definitely top 5 boss battles of all time.
Adam @ Apr 22nd 2008 9:25AM
Some of my most recent boss fight memories are from the Metroid Prime series. Metroid Prime 2 had a very hard final boss fight which I never beat (I still need to go back and do that), but I think I beat Prime 3's final boss first try.
I agree with Mike D on Galaxy, that was way too easy.
The boss in Portal wasn't too bad. Had an awesome ending song, that's for sure.
I always liked the final boss in Ocarina of Time, where you jam the master sword through Ganon's head at the end.
Oh, and mother brain in Super Metroid was awesome. Where the huge metroid comes and sucks the juice out of her and gives it to Samus. Then Samus has that badass rainbow gun. Good times.
Looking wayyy back, I never did beat mother brain in the first metroid.
samfish @ Apr 22nd 2008 9:31AM
The best two boss fights for me would probably be Devil Hand in God Hand and Gannon in Wind Waker.
Wind Waker because when I fought Gannon the first time, I remember being shocked that he was fighting back and blocking my attacks with his sword. It's the first time I ever experienced that in a game and it just blew my mind. I actually felt like I was having a sword fight.
Devil Hand because that was just pure awesome. The first time he pummeled me I was thinking, "He's pummeling me?". I was quite confused, but and I then realized I could hit back. Even though I was alone at the time, I remember laughing and saying "No way! Awesome!" when I started pummeling back. This was all within a span of about 3 seconds, tops.
...plus, he was hard as freakin' hell and it was soooo rewarding to finally beat him (both times).
samfish @ Apr 22nd 2008 9:41AM
Also, I should give props to Okami's final boss. It was a nice, looooong fight that made you think about how to beat him.
Plus, the entire sequence was just epic on a scale I've never felt before *cough*itmademecry*cough*
Yet another reason to buy Okami (on the Wii) for anyone who hasn't yet.
SoshiKitai @ Apr 22nd 2008 12:26PM
Devilhand was pure awesome. :D
And kickin' him in youknowwhere was just as fun!
CJLopez @ Apr 22nd 2008 2:27PM
Damn, DevilHand, that was a fight, it was awesome when the rapid smashing button attack, that putted my adrenaline pretty high!!!!!!
Roto13 @ Apr 22nd 2008 9:32AM
I liked the final boss of Wind Waker. It was really epic.
Also, the final boss of Portal was awesome. :P If only for the random quotes.
Guitar Hero III's battle with the devil playing The Devil Went Down to Georgia was pretty awesome, too.
Max @ Apr 22nd 2008 9:34AM
Ganon at the end of Zelda: A Link To the Past. Since that was one of my first games he was so hard it was scary.
Yeah, Joystiq's right about No More Heroes. Took me a while.
Prince of Persia 3! Wanna fight the final boss? You'll lose! You have to run away from him. What fun.
Super Metroid pretty much speaks for itself.
Yoshi's Island's final boss was pretty crazy when it came out. I remember being freaked out when he just starts charging at you nonstop and desperately throwing eggs at him.
Majora's Mask has one of the best boss battles in the series. Goht. Thank god for time travel, I could always play him again if I wanted to.
Nicholas Tam @ Apr 22nd 2008 9:36AM
As formulaic as it has become for bosses to take on multiple successive forms, I'd have to agree that the final sequence of Twilight Princess exhibits a sense of escalation like almost no other game. I think lot of it lies in the way it requires you to deploy such a variety of skills, kind of like a final examination of what you've learned.
Of the previous generation, though, any discussion of iconic boss fights begins, and perhaps ends, with Viewtiful Joe's Fire Leo.
Nigeria - MK: 0430-8491-9123 @ Apr 22nd 2008 9:36AM
Speedbuster from NMH was an epic battle. It wasn't the best boss on the game, or the most challenging, but the position the game put you in - one small man against an incredibly overpowered laser beam - made it the grandest battle. I loved it. If NMH had boss battle option??? I'd surely do that boss over and over again.
I really loved Donbalon from Nights - which was basically a remake of the first boss from the original Nights game. The name escapes me now, but I liked that little nostalgia trip. And, I liked the Chameleon, even his hiding antics really pissed off my friend.
The greatest boss battle I remember is from the greatest game of all time: Sonic & Knuckles. The first time you face Robotnik, I think, you're constantly running in a forest and you have to attack Robotnik while avoiding different barbed balls. And the music's pumping. It's a really great opener.
Mr Khan @ Apr 22nd 2008 5:11PM
You liked that Chameleon? Damn. That was just the definition of frustrating, especially since failure meant re-doing the entire stage
Out of that game, i particularly liked the spider, Helen's third boss, whatever its name was
coleduke @ Apr 22nd 2008 9:36AM
Beating Ganon in Zelda: A Link To The Past is probably the most memorable for me.
Patrick @ Apr 22nd 2008 10:17AM
I'd have a hard time choosing a favorite boss from NMH. The final boss was sweet, but there were so many other good ones >_<
Fighting Gandrayda in MP3 was intense, also fighting the final boss was pretty tight too.
sly @ Apr 22nd 2008 10:32AM
Sigma at the end megman x2 and x3
Author X @ Apr 22nd 2008 10:36AM
A LOT of memorable bosses in NMH, too many to list... *spoiler* was particularly pressing, because the way dodges just almost everything, even after dark-stepping or stunning her, and turned my wrestling moves (my favorite for bosses) against me just freaked me out and put the pressure on me.
However, for all-time favorite boss fight... The End from Metal Gear Solid 3. It may just be because the first time I beat him was particularly spectacular, but the length and intensity of the sniper battle was just amazing.
The first time I beat him, I was going for a stamina kill, which means only tranquilizers and hand-to-hand - and the only tranquilizer sniper rifle in the game is the one HE's wielding, which is the reward for the stamina kill. Meaning I had to find him, make the approach unseen, and sneak up close (I was also trying to hold him up to get his camo and what-not). This was all in an arena spanning THREE maps, with sniper points hidden in each one, overlooking most of the map and usually a good portion of the other two. He wouldn't even show up with thermal goggles, because he lowers his body temperature once he's settled in! And until you get his health/stamina down, he lowers his breathing to practically silent. The best part... you can see the glint off of his scope... but even if he hasn't seen you by then, HE can see the light reflecting off YOUR scope if you're looking through the sniper rifle or even binoculars! If you were looking for him with either of those, you had to make sure than not only are you well hidden, but there's no sunlight falling on your hiding place! It was really the ultimate boss fight in a game about stealth, camouflage, and espionage.
And as for my personal experience... I had to have been wearing him down for an hour (okay, MAYBE half an hour and it felt longer... but I still think it could have been an hour or longer, it felt like two hours), and realized that I would have him in three more tranqs. So, yet again, I tracked him down, snuck up, and pulled the trigger three times... and got *BANG*BANG*click*
Yep, I ran out of ammo at the last shot. I freaked out and just started chasing him around, punching him, but soon realized that while you can take a boss's stamina down with a choke-hold or hand-to-hand or other CQC attacks, you can't finish them off! It has to be a tranquilizer dart - of which I had none.
It's also worth noting here that if you leave him hiding too long, he can also call upon the forest to RESTORE HIS HEALTH AND STAMINA. Yep, so I had to keep chasing him around, punching him in the face, because I was afraid that if I lost his trail (once you find him, you can follow his footprints with thermal goggles if you're fast) I'd lose him and he'd regenerate, really making all that work futile (f***ing druid...).
Finally, I remembered... in the first map, the southern one where you start, there's an ammunition bunker in the south-west corner! Surely it would have tranquilizer darts! So I caught up to The End once more, punched him in the face, and ran south as fast as I could. It's been some time, but I believe there was ONE clip of tranq. darts, which meant I had to make sure to find him again before he restored his stamina. Fortunately, I managed to do so, and took him out non-lethally... so that I could watch the cutscene where he explodes dramatically, like all the bosses in that game.
A lot of people complain about the long ladder that followed that boss fight, but I really needed it for exactly its purpose - a long, relaxing cooldown after an incredibly intense battle... you know, so I didn't have a heart-attack right there. I mean, seriously... holy crap... greatest boss-fight in my gaming career. It felt like it took hours. I can't believe some people skipped it entirely (well, actually I can understand why they included the option for people that don't want such a huge challenge... I can easily imagine someone that plays the game casually spending an entire week trying to beat The End and discovering the shortcut that way!)
SoshiKitai @ Apr 22nd 2008 12:55PM
The shortcut's hilarious, though! XD
Seeing an old man in a wheel chair blow up was one of the most hilarious things I've ever seen.
Author X @ Apr 22nd 2008 5:07PM
Actually, I meant what happens if you save in mid-battle, then load with the PS2's clock a week ahead of the date you saved. But that's fun too :P
bearmedal @ Apr 22nd 2008 10:53AM
Hoo boy, where to begin...
Viewtiful Joe 1 & 2 - Another Joe kicked my ass three ways 'till Sunday, and had my favorite music in the game. In the second, Jet Black gets my pick 'cause it's Joe's father, it takes place in the real world, and it too has my favorite music in that game.
Mario and Luigi - For Superstar Saga, I'd say it's seeing all the Koopalings return after a too long hiatus, only to be followed by an amazing Fawful battle, which is then followed by a seriously challenging final boss.
As for Partners in Time (aside from the bosses having good music) I say the Shrooboid Brat (it makes excellent use of the top screen), and the final battle against the elder Princess Shroob atop that spaceship-thing.
Zelda - Twinrova was my favorite for a while, but it got dethroned by Stallord, Argorok, Ganon/Ganondorf, and pretty much every boss from TP. Yes, most were easy, but they all were so much fun! Honorable mention goes to WW for Molegra (kick-ass music) and Ganondorf (an actual swordfight instead of an item-filled fight a la OoT, and it has a finish that made me shout in surprise).
Sonic - Lava Reef Zone in S&K is still one my top favorites because it starts with a chase scene through a waterfall of lava, and you win not by fighting, but by surviving. Also from that game is Doomsday Zone, which is a legendary fight.
Honorable Mentions - Omega Pirate (Metroid Prime), the Nightmare (Kirby's Adventure), Abyssion, the Summon Spirits, and Mithos (Tales of Symphonia), and, of course, Bob the Goldfish in both Earthworm Jim games.
(*whew*)
Moose @ Apr 22nd 2008 11:19AM
I had a hell of a time with Argorok but I think that was the most satisfying boss battle in TP.
Croove55 @ Apr 22nd 2008 10:55AM
Since my first final boss was Super Mario 64's Bowser, I'd have to say that he'd be my favorite. I was expecting his normal hard rock song to come in, but no. You get hit with some of the most terrifying organ music you can imagine, and bowser is lit with eerie, other-worldly multicolored light. The entire fight is on a platform in a darkened, violet/black sky, and bowser gets up from two hits that have taken him down in previous fights, and then proceeds to destroy the platform with pure rage. It was incredibly intense when I was about 7 years old.
Other games with great final bosses would be
No More Heroes (Both of the final bosses)
Kirby 64 (Hidden Final Boss, so glad they put his theme in SSBB)
Entire Metroid Prime Series
Twilight Princess and Wind Waker
After looking through my GBA catalog, I'd like to change my favorite boss from SM64's final Bowser to Golden Sun's boss. The song on SSBB might not even do this one justice, it's that amazing.
jaredgood1 @ Apr 22nd 2008 11:15AM
Kain vs. Raziel in Legacy of Kain: Defiance. You get to play as both characters (Kain first then Raziel) and it's kinda fun to be on the receiving end of some of the punishment you've been dealing before the fight.
Star Wolf in Star Fox 64. Awesome, awesome dogfight.
Ghost Train in Final Fantasy 6. When you first think "hey, it's a ghost, I wonder what a Phoenix Down will do", so you try it and it instantly dies... brilliant.
and let's not forget Psycho Mantis. "Snake, you've got to plug the controller into slot #2". Fun, functional and a nice way to break the fourth wall.
Orion @ Apr 22nd 2008 11:17AM
im going to be a bit creative with mine. While the above game bosses are great, there are many more that have been memorable to me.
First up I'd have to say the final fight with Andross in the Super Nintendo version of Star Fox. While the 64 version was nice, the super nintendo game, in all the bosses really, gave you a much larger sense of urgency. I think the music, feel, etc, just made the game overall much more darker, which i love still to this day (hope they put starfox on the VC for the super nint).
Second would probably be beating Roadblasters on the NES. I know many have not heard of this game, and i know it's not a true "boss battle"... just the enormous difficulty of having to race PERFECTLY and get EVERY fuel cell on the road made me so proud of myself when I beat it back in the day. I really love that game, another I wish was on the VC.
Third would have to be Super Mario RPG. MY GOD was that a hard fight at the end. And if you weren't leveled up enough by the time you got to the boss, you were pretty much screwed.
Some other honorable mentions would probably be beating F-Zero X (now it's not so bad, but when I was younger when it first came out, it was my first 64 game.. and it blew my mind). I've never beat a zelda, kinda hoping TP will be my first lol... i hardly ever stick around or have enough patience for long games. Kingdom Hearts II was an entertaining end boss battle though. Super Mario Bros 3's end was VERY fun. Oh and just to end it on the Saturn, Gundam Side Story III's end boss was an utter blast with the Virtual On sticks.
Hmm... I think I'll leave it at that for now.
Author X @ Apr 22nd 2008 11:56AM
One thing lacking with SNES Andross.
Only /I/ have the brains to rule the Lylat system!
kastonie @ Apr 22nd 2008 1:22PM
yea dude.... I'd have to agree with you on andross in teh original star fox....that was one of the best in my opinion. i remember feeling my adrenaline rushing as i fired the last shot and defeated him and watched the ending cut scene with my arwing blasting through the tunnel while it was exploding around me...good times....
Orion @ Apr 22nd 2008 1:43PM
haha yea i know what you mean. and remember the end credit music? wasnt it so much cooler back then? It had a serious, almost techno/military sound to it.. was nice.
I'm hoping that with the release of mario kart wii showing n64 style music, that in the next starfox, they will revert back to the old feel when it was less about cartoony mascots and more about the urgency of the situation and the white knuckle airwing game play (armada was horrid in that respect. it was an ok game, just not when compared to other star fox games).
Tesche @ Apr 22nd 2008 11:18AM
i can't believe no one has mentioned Shadow of the Colossus yet....though that is almost like cheating on a question like this....the who game is boss fights after all...but i haven't been that shocked by a final boss in my life I don't think. A completely surprising ending.....
Honorable mention goes to Portal for memorability.
I realize that I haven't mentioned a nintendo system game yet, so in that arena, I'd have to go with.... honestly, I try to come up with something else, but I keep coming back to the final boss of final fantasy II on the SNES because the payoff was so amazingly worth it. It was the best story telling that I'd encountered in a game at the young point in my life.....
SoshiKitai @ Apr 22nd 2008 12:30PM
Shadow of Colossus had epic boss battles (then again, that's all they were)... and the surprise final boss was definitely something new and surprising!
--but as impossibly hard boss fights go - Nope, they were just extremely dramatic and heart-pumping.
Moose @ Apr 22nd 2008 11:22AM
I think your first boss battles are always the most memorable. I remember my first fight with Ganon on the Legend of Zelda and Mike Tyson on Tyson's Punchout.
I really enjoyed the Nintendo Power feature where you take a photo of the final screen from a game, send it in and get your name in the mag. I used to think that was the coolest thing in the world.
GatorSax2010 @ Apr 22nd 2008 11:53AM
The entire Ganon/Ganondorf sequence in Twilight Princess was great, and I had a blast fighting the Stallord. The fight against Meta-Ridley in Metroid Prime 3 (the Balrog-type fight) was also awesome. And who could forget Psycho Mantis... I already knew all of his tricks when I fought him, but it was one of the best fourth-wall breaking, mess-with-your-head boss fights I'd ever seen.
Jay @ Apr 22nd 2008 12:13PM
You've been playing Twilight Princess.....couldn't resist
and Omega Ridley was fun.....take the tried and true Ridley strategy (the one where you just keep shooting till it dies) and add X-Ray vision
MRB1G @ Apr 22nd 2008 12:07PM
Every single boss in Legend of Zelda from Ocarina of Time to Twilight Princess (excluding Four Swords and replacing it with a Link To The Past) was amazing for me, but Super Mario 64 with Bowser has to be my favourite as he was the first boss I ever faced: I was blown away.
Other favourites: Dark Samus in Metroid Prime 3 Corruption, (the incredibly easy) Bowser from Galaxy and the many mind boggling bosses from Zack & Wiki
Jay @ Apr 22nd 2008 12:10PM
Stallord in TP was just freaking epic. When I first got the spinner I was like "WTF, what use is this"....and then that
Then both forms on Ganon in WW. Puppet, because he pissed me off so much in having to freehand aim.....Ganondorf, despite the PRESS A TO WIN was just cool to watch
SoshiKitai @ Apr 22nd 2008 12:44PM
Boss from MGS3... I had to say, it was one of the few games where the final boss WAS ACTUALLY AS GOOD AS YOU WERE.
She didn't have impossibly hard stats, or have skills that were impossible to get through: She had as many weaknesses and strengths as you did, and in the end - the better would win.
--for me, she wasn't EXTREMELY HARD, but she was so much fun! It felt like a real final battle! Like a real test of skill! Not some "Oh I'm a boss with specific weaknesses, raarr!"-battle... it was a real fight! With a heart-wrenching ending to go with it.
Oh... and The End in MGS3, he was pretty tough too. He was "easy" if you watched and listened, but it's fun to watch impatient people fight against him! Note to all who are impatient: Fight The End on the hardest difficulty and you are sure to die. 100% sure. XD
Who did I hate fighting?
Hmmmm... most KoF bosses were impossibly hard for me.
And for someone like me who's not that skilled in fighting games, some boss fights in Guilty Gear (more recent ones) killed me.
I know Dr. Mario 64's final boss was pretty hard.
Oh, and Lavos in Chrono Trigger! If you accidentally took the shortcut like I did - you'd end up dying pretty quick too. And even if you didn't, he was still pretty darn tough.
Oh, and the "king" in Tactics Ogre? Tough as heck, I nearly got some of my men killed in that battle! (Note to others: I NEVER let my men die unless it's a necessary sacrifice)
Oh! And in Guardian Heroes, the final bosses weren't impossible, but they were tough and fun to fight!
As you can see, I'm not much for the "I'm impossibly impossibly powerfully tough boss with specific weaknesses"-boss fights... I'm much for that "I'm just as tough as you, kid"-boss fights.
Now, an example for the kinds of bosses I hate to fight:
http://youtube.com/watch?v=sQZuidKexBQ
SoshiKitai @ Apr 22nd 2008 12:46PM
I forgot to mention:
I hated fighting Smithy in Super Mario RPG.
Orion @ Apr 22nd 2008 1:44PM
haha i meantioned that in my post up above. if you werent level 30 you were pretty much screwed from the get go. lol
SoshiKitai @ Apr 22nd 2008 5:00PM
As Luke reminded me:
The fight against Luca Blight in Suikkoden 2... that was insane. :D
zeldazeppelin @ Apr 22nd 2008 1:56PM
tp final boss fights and metriod mother brain
hvnlysoldr @ Apr 22nd 2008 2:24PM
I haven't been able to replicate my fight against Bowser in the Fire Sea. While he's teleporting around all invisible I grabbed his tail at his landing just before he turned visible again. It was awesome to throw the invisible Bowser into a bomb.
CJLopez @ Apr 22nd 2008 2:55PM
Here I go
Ganon in Zelda 1, Link to the Past, Ocarina of Time, Minish Cap, Oracle of Seasons and Ages, Twiligth Princess and Link's Awakening
NHM - Shinobu, that was a sword fight, also Holy Sword was thrilling, the bomb chick was pretty funny battle, Jeanne, man, what a fight, but my favorite was *BEGIN SPOILER ALERT* the final battle against Travis twin brother (sorry, i'm bad with names). That was a Fight i did enjoy a lot *END SPOILER ALERT*
Super Mario RPG - Against the arrow like enemy. Disabling commands was pretty annoying, still, you just have to come up with new strategies each round
Final Fantasy - 4 - Final Boss, 6 - Kefka's Final Form, that was a cool battle while not using any cheats or nothing, just replacing fighters along the way, 7 - the weapons, man, pretty hard battles, using the final summons made me nearly beat em. Also, Jenova's final form, before fighting Sephirot's final form, that battle was awesome, switching from teams.
God Hand - As i said before, DevilHand battle was, man, that was the battle of the game, also, the final battle against Magara using *BEGIN SPOILER ALERT* the 2 god hands, that double shaolin blast was amazing. I'd like to be a second part of the game *END SPOILER ALERT*
Kingdome Heart - What can I say, on the first one, the final battle was amazing, and fighting against Sephirot was almost a dream come true. And on the second, Sora and Riku at the same time and changing in middle battle from Sora to Riku, what else can we ask
Doom - Every final boss
Wolfenstein 3D - Beating the crap out of Hitler was hillarious
There are many more, but i'd spent the whole day posting em here
andy @ Apr 22nd 2008 3:58PM
I'm having a bastard of a time with Destroyman from No More Heroes. Its just such a boring fight that I don't really care enough to get into the action and actually try to beat him.
SoshiKitai @ Apr 22nd 2008 4:56PM
He's annoying... REALLY annoying: That should be enough excuse to bring him down.
Dio @ Apr 22nd 2008 4:35PM
Tales of Phantasia - Dhaos
Any of the Castlevania games - Legion, Chaos, the GOOD Draculas
Ouendan 1+2 - Final songs
Megaman Battle Network 3 - Serenade and BassGS
Kingdom Hearts - Sephiroth and Ansem
Starfox 64 - Rival fights, true Andross
I'm sure there are others, but they were too long ago.
Luke @ Apr 22nd 2008 4:38PM
I thought the Bowser in Super Mario World was pretty awesome. He wasn't to difficult, but it was a perfect cap to the game, with the lightning on top of the castle. Also the clown ship was a good touch. The best part was the music as bowser floats in though. Also the princess throwing you mushrooms was awesome. Maybe it was just because I was like 5 when I beat the game, but I thought it was pretty dramatic when she yelled HELP!
Luke @ Apr 22nd 2008 4:42PM
oh, and the boss in Suikoden II was epic, especially Luca Blight. (If you didn't play the game, it took three parties of 6 characters to beat him, which was HARD!)
SoshiKitai @ Apr 22nd 2008 4:59PM
OMG! I can't believe I forgot to mention that!
That was so fun!
For me, I could've easily beat him with just 2 teams, but I went easy on him because I was being cocky.
But yeah, THAT was an awesome fight! HE TOTALLY WAS BUTCHERED!! (especially with the archers and all) ... it was kinda' sad at how he had no chance, though.
Mr Khan @ Apr 22nd 2008 5:17PM
Metroid Prime from the original Metroid Prime, one of the few final bosses i've felt compelled to fight time and again, for the great thrill of it
I also liked Miracle Matter in Kirby 64, the Egg Emperor (final boss of each story in Sonic Heroes), the Ghost from Wario Land 2 (the one that was tied to a bungee string and kept trying to grab you), final Bowser from Super Mario Galaxy, and Drawcia from Kirby Canvas Curse
One thing outstanding about Kirby games has always been the bosses
Nigeria - MK: 0430-8491-9123 @ Apr 23rd 2008 5:59AM
Oh man, I totally forgot about Kirby.
I just completed 64 on the weekend so I saw Miracle Matter: that was a BOSS battle, in the full sense of the word. It was so difficult, compared to previous Kirby encounters. But I liked the challenge, even if it took me 7-8 retries.
I don't have a favourite Kirby boss battle - they're mostly pretty cool - but I like seeing the reoccurring tree character. It's a poor challenge, but I like it: memories from Dreamland on the GB come flooding back. It's a nostalgia thing.
Haohmaru @ Apr 22nd 2008 5:57PM
Sheesh! It looks like everyone has already posted my favorites, but I'll list them anyway.
Legend of Zelda: Wind Waker - Gohma. I loved swinging over him on Valoo's trapped tail.
Legend of Zelda: Twilight Princess - Morpheel and Argorok were tremendous fun.
Final Fantasy 6 - The three-part boss that looks like a twisted painting before the "real" final battle with Kefka.
No More Heroes - I always HATE fighting the #1 Ranked assassin. (I find the "real" final boss extremely fun, on the other hand."
Star Wars: KotOR - Darth Malak. It just felt so epic and dramatic - the revived Master taking on his former Apprentice.
Super Paper Mario - The entire Duel of 100. xD