I mention this one everytime we do this topic but its still up there as my all time favourite boss battle.
Sonic AdventureSuper Sonic versus the massive 'Perfect Chaos' beast.
The fight just had that perfectly epic feel to it. You, versus this massive fucking behemoth of a thing that just levelled a city pretty much by accident, streaking towards it and weaving in and out of its attacks in an effort to smash the bastard in the brain before your collection of rings runs out and consigns you to a watery death. You were totally capable of destroying the thing, but you had to be quick about it.
The music, as cheesy as it was, was the perfect accompaniment to the on screen action. One of the things that was so great about it was that for a limited time you were this blazing ball of pure energy, as powerful and as unstoppable as the boss before you - save you were on that ring enforced time limit.
Metal Gear Solid 3 Naked Snake versus The Boss.
This wasn't a paticularly difficult battle (Easy to break since you can just drop some mines and let Boss come to you) but its one of the most atmospheric boss fights you can find in a game, especially when taking into account everything that's happened up untill that point and its ending, that damn ending to the fight which I witnessed take one of the most manly people I've ever met in my life and reduce him to a blubbering ball of muscly emotion. You haven't seen an MGS fan untill you've met a mad Welsh fitness instructor named Barry who lives, breaths and eats the MG franchise. He has MG brand coasters! (Actually just pre-owned MGS1 discs but still.)
Resident Evil Player versus the Shark.
Its hilariously pathetic. Whoops you just dunked a portable generator into the tank and fried the chap before he had to chance to have you for seconds. (If you're playing as Jill)
Streets of Rage 2 Player versus Mr.X
Can you imagine the dev's thinking this one up? "Let's give the only gun in the city to the final boss, then make him go ape shit after you take down his right hand man and have bugger all health left." This one's in the list just because of how brutal it is on mania mode.
Street Fighter 2: The World Warriors Player versus Dictator
I specify World Warriors edition because Balrog/Bison (we'll use Dictator) was toned down a notch with each update to SF2. But in WW, you were basically up against a heat seaking missile dressed like a dictator for the evening. Left right left right like an ink jet bloody printer until you were down for the count. Blocking was no good since he'd pass through your hit-box and his feet hitting your waist was counted as a back attack. If you didn't pay attention to what was going on, you were dead. Which is how a final boss battle should be done.
Dead Rising Frank versus Brock.
Fist fighting on a tank surrounded by billions of Zombies. Who doesn't want to do this? Even if you lose, its the manliest damn way to die, ever.
Guilty Gear Player versus Justice
Yeah...just try doing this without Ky, Sol or Chipp.