Here's the best of the best that I've encountered!
Andross/Escape from Venom (StarFox 64/N64)
Baby Bowser (Super Mario World 2: Yoshi's Island/SNES)
Bowser (Super Mario World/SNES)
Bowser (Super Mario 64/N64)
Bowser (Super Mario Galaxy/Wii)
Bowser (New Super Mario Bros. Wii/Wii)
Bowser (Super Mario Galaxy 2/Wii)
Gary (Pokemon Red/Blue/GB)
Ganondorf/Gannon (The Legend of Zelda: Ocarina of Time/N64)
Ganondorf (The Legend of Zelda: Wind Waker/GCN)
Gannon/Ganondorf (The Legend of Zelda: Twilight Princess/Wii)
Meta/Omega Ridley (Metroid Prime 3: Corruption/Wii)
Metroid Prime (Metroid Prime/GCN)
Wizpig (Diddy Kong Racing/N64)
So out of those contestants... the winner is:
Ganondorf/Gannon (The Legend of Zelda: Ocarina of Time/N64)
This is the best boss fight I've ever played. You climb a seemingly endless tower (while the organ is playing), you engage in great fight, swatting away energy orbs, you make him puke (green) blood, you escape a collapsing tower, and then you engage a terrifying beast in combat for all the marbles. I haven't experienced anything like it before or since then (Twilight Princess' final battle comes close though!)
