Hmmmmmmmmmmmmmm....
- The God-Generals from Tales of the Abyss all get cookie points, but I enjoyed fighting Legretta and Sync most of all.
- Gaius from Tales of Xillia is a step up from the rest of the game's bosses but he always puts a smile on my face. The Chimeriad fight in the coliseum would be up there if not for the fact that the game lags horrendously each and every time there.
- Amber from Tales of Graces. She's fast, she can combo you to death, but she has reasonable weaknesses to make for an interesting fight.
- The Four Stars altogether in Tales of Rebirth, because they complement each other so well. I always love finishing the fight with a Mystic Arte.
- Each and every incarnation of Ethereal Queen, since her theme
never gets old (insert Sakuraba gushing). Her SO 3 incarnation is sadly the weakest of the bunch, but the game at least has tougher bosses to throw at you. 
- The battles against Astaroth in Shadow Hearts. Great chance for comboing, amazing theme and reasonably challenging.
- The Reaper from Persona 3 and 4. His AI got stupider in Persona 4, but in 3 he's deadly.
- Croselle from Star Ocean 3. Kickass theme, hits like a truck, but I get to spam Side Kick, so all's good.
- The first fight against Lezard in Valkyrie Profile 2, since I get to use all three Valkyrie sisters without being stupidly overleveled.
...That's at the top of my head, anyway.
"If you aren't him, then you apparently got your brain from the same discount retailer, so..." - Fighteer
Artorius from Dark Souls DLC.
and because im feeling uncharacteristically nice towards abyss right now, the nebilim boss fight, which was the only human boss fight in the game where i didnt notice some fuckery with the limits.
ASSUMING DIRECT CONTROL
Big Arm from Sonic 3 (sans S&K). The sky darkens, that theme kicks in. Love it.
Champion battle from Pokemon Red/Blue. A bit less so these days since I'm much better than I used to be so the challenge is a bit lost, but still.
Absolutely no relation to NLK
Many Duel Bosses. Vergil from DMC 3, Credo and Dante from DMC 4, Riku-Ansem from KHI, half the bosses in KH:COM, Roxas from KHII(FM+), all final bosses in KHBBS...
Dopants: He meant what he said and he said what he meant, a Ninety is faithful 100%.
Twinrova from Ocarina of Time and General Guy from Paper Mario. I have files saved before those two so i can fight them whenever I want.
The Protomen enhanced my life.
M.A.C.E from Intrusion2. Too epic for words. And it's made on Flash apparently, so it's the most epic flash game boss ever.
His background laser/missiles move reminds me of General Tor, except even more epic.
edited 8th Dec '13 3:51:52 PM by ironcommando
...eheh
Taller than Zim
KING OF EXPLODO KILLS
Armstrong from Metal gear Rising. He's one of the hardest, most gratifying bosses I've ever fought, and he's even better when you fight him as Sam!
nyo ho ho
Komato Annihilator Iosa (Iji): As you play the game, you'll find that Annihilator's are things you should run from fast. They're huge, have a fudgeton of health, and can kill you quick. This time, there's no turning back. Iosa has a energy spreader (kinda like a flamethrower), an MBF Devastator, and even a Velocithor V2-10, by far the most powerful weapon in the game! And when you're through with her, you have to take down her true form, which is COMPLETELY invincible outside of cracking her nanofield. The whole thing gets exponentially more epic with Anaksie helping you.
And then there was silenceSuper Power Robot Ninja Yokozuna and GTR from Contra: Hard Corps. Their animations are very good, and the boss fights are pretty awesome (one races the train and stops it, the other is a Combining Mecha). They have a pretty epic boss theme too.
Not exactly a favorite boss, but this is one of the most hilarious names of any boss I've fought:
"Kommie Kong" from Heavy Weapon. The Dirty Communists + King Kong reference couldn't be more blatant than that.
edited 8th Dec '13 5:49:49 PM by ironcommando
...eheh
Fandom Heretic
Metal Gear Solid: Vulcan Raven. Nuthin' like cruising around laying obvious C4 traps to blow up the enemy.
Some additional ones for me are Xemnas from Kingdom Hearts II and Munenori Yagyu from Onimusha 4.
EUREKA!
Dark Bowser, 02, Kefka, Dreamy Bowser, Solaris, and Egg Nega Wisp because dat music.
Perfect Dark Gaia because awesome final boss.
Marx Soul, Perfect Chaos, Finalhazard, and King Dedede because nostalgia.
edited 9th Dec '13 2:21:00 PM by DiscoDancer
Your Honor...
Ghosts N' Stuff Remix
This barely counts as a boss fight, but I really loved all the Future Unraveling puzzles in Mystery Case Files: Madame Fate. Basically, you collected a bunch of hidden objects to look into the future of all these creepy carnies to find out who kills the fortune teller at the stroke of midnight! And there are these great puzzles with this sort of circus-poster aesthetic to them, and they were all really clever, despite the fact that they were minigames. My favorite one was the Tattooed Man puzzle, because it was really vibrant and colorful, and required lateral thinking.
"Monsters are tragic beings. They are born too tall, too strong, too heavy. They are not evil by choice. That is their tragedy."
The Emerald Weapon from Final Fantasy VII. Taking that bugger down felt like a real achievement, given all the hoops you have to go through to get the One Item that enables you to have a realistic chance at kicking him in his giant sized goolies. The Ruby Weapon fight was trickier but didn't take as long all things considered.
Blowout soon fellow Stalker
Senator Armstrong and Metal Gear Exelsus from Metal Gear Rising Revengeance
Just everything about that was great.
Hell, all the bosses were great fun.
edited 11th Dec '13 8:08:00 AM by LeGarcon
Oh really when?
Brightness
From Metal Gear (in no particular order):
- Rex v. Ray
- The Boss
- The End
- Rex
- Peace Walker (second fight)
- Zeke
- Liquid Ocelot
- Mass Production Rays
- The Sorrow, if that counts
- Everyone in Metal Gear Rising Revengeance
Lavos from Chrono Trigger.