Can't narrow it down to just one, so I'll just post a bunch of ma' favorites.
Metroid Prime 2: Echoes - Emperor Ing 2 Battle (Yes, I know that technically, Emperor Ing wasn't the final boss of Prime 2, Dark Samus was. But damn it, this song is better, so shut the hell up.)
The Legend of Zelda: Twilight Princess - Ganondorf Sword Fight
Shadow of the Colossus - Demise of the Ritual
Sonic & Knuckles - Doomsday Zone
Kingdom Hearts II - Darkness of the Unknown
Super Mario Galaxy 2 - Final Bowser Battle
Super Smash Bros. Brawl - Tabuu
Crash Twinsanity - The Evil Twins (Yes, I'm serious. Twinsanity had some GREAT music!)
Mario & Luigi: Bowser's Inside Story: Final Battle
Sonic The Hedgehog (2006) - Solaris Phase 2 (Yeah, yeah, yeah, the game was awful. But it did get one part right: The music.)
Long-ass list, I know. Yet I still feel like I'm forgetting something...
