Ornstien and Smough from Dark Souls, Such a fun fight cause it's a fight that totally odds against you and you learn to beat it eventually.
Fume Knight in Dark Souls 2 was amazing and scary and fun.
Chiaki in SMT Nocturne, lots of great bosses in the game and this one is my favorite from what i remember.
Koloktos from Skyward Sword. Wasn't mind blowing or innovative, but it just had the perfect atmosphere and was very fun to fight. I think my favorite kind of boss is one that acts like a puzzle, where you have to figure out their weakness in multiple steps. Of course, while feeling the pressure of them constantly attacking you!
This might be an odd one, but probably Barinade from Ocarina of Time. That one sticks out in my memory, anyway. I have the biggest urge to play that game again now.
Another mention is Grunty at the end of Banjo Kazooie. That's the longest, most drawn out boss battle ever. The battle music is an awesome mash up/medley of all the world themes that came before it, you've got to use EVERYTHING you've learned to defeat her and- even if you get all the health upgrades at the end of the game, the final phase when you've got to awaken the statues is fucking HARD. You're being atacked left right and centre, if you make it out of that in one piece, you're very lucky.
Yeah I'm going to change what i said and go with the boss in mgs3.
Albeit it was the easiest boss in the game, it was still a tense and really artistic way to finish one of the best spy games ever made.
I was actually bitterly disappointed with him. After all the glory, it came down to a "fire;duck behind cover;repeat" scenario. Much like that fat sack of alien shit at the end of Borderlands.
I always found the Patriarch in Killing Floor to be a pretty fun boss. If you do it just right, you can kill him with a knife. But fuck up once or twice, and you'll be annihilated. A bit like a lot of the bosses in Dark Souls I guess, though I'd hate to take on the gargoyles with just a knife.
Lord Vanaduke from the game Spiral Knights. Gaaaaawwwd it took me so long to finally beat him, so many revives ._. Jeez. The music and the whole fightnwas just intense, Slag Guards and Slag Walkers charging at me constantly and fire falling from the collapsing ceiling and even mor fire from Vanaduke himself ._. A giant mace slamming down on you. Jesus, the fight almost gave me a heart attack, but I loved it...
This is kind of a weird one, since it's a bit of a cult hit, but Brayko from Alpha Protocol. A Russian gangster obsessed with the '80s, you fight him in a personal disco, with "Turn up the Radio" by Def Leppard as the background music. Cocaine is his power up. It was actually pretty difficult to kill him, since if he gets in close he can kill you easily if you're not careful. However, if you wanna do some sneaky spy shit, you can poison his cocaine supply before the battle. Also, as a reward for beating him, you get a memento of his purple leopard jacket, with additional snide dialogue. I think the only thing that would have made this more epic was that originally they were going to play "The Final Countdown" as the background music.
Probably not the best boss battle I've played on a technical level, but probably the most memorable, and I absolutely love that game (where else are you going to have Nathan Drake come by and shoot a bunch of bad guys from a Gatling gun on a subway train, and throw an Osama Bin-Laden proxy of a bridge while saying "Remember how you used to pretend to play airplane when you were a kid? Well now we're gonna do it for real"?)
My choices are based on the plot of the stories of said games. Most are emotionally charged and the rest were just fun.
In no particular order:
-(Another Vote) The Boss from Metal Gear Solid 3
-Sniper Wolf in Metal Gear Solid 1
-The Elements (Voltron type Gear) in Xenogears
-Frederic Chopin from Eternal Sonata
-Roxas in Kingdom Hearts II Final Mix
-Serge vs. Lynx (After Switching Bodies) in Chrono Cross
-Ven vs. Vanitas in Kingdom Hearts: Birth by Sleep
-Angeal in Final Fantasy VII: Crisis Core
-Topo in Brave Fencer Musashi ((Always loved a good dance battle))