Mother Brain from Super Metroid.
The Boss at the end of MGS3 was an epic battle, mainly for the emotional factor. Other than that, I haven't really been impressed with any other final boss battles.
Aphelion from Radiata stories is the only good answer here.
To me, it would have to be Braska's Final Aeon from FF-X.
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For some reason, I really liked the battle against the kind-of-aptly-named 'Giant Tree' at the end of Suikoden IV, although they never really explain why it's there in the first place...still fun, though.
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I'm going to have to go with the series of battles against Ganondorf in Twilight Princess. First the battle against Puppet Zelda, in which there's the bit of a throwback to the battle against Ganondorf in Ocarina of Time. Next there's the battle against his beast form, the new interpretation of Ganon (although I do prefer his form in OoT). The battle on horseback is pretty awesome, too, but what takes the cake is the one on one sword fight at the very end.
Hitler II in Bionic Commando.
So many:
Tower of Kefkas! (FFVI), Sephiroth (FFVII), Lavos (Chrono Trigger), Metal Gear (Metal Gear Solid), The Queen (ICO), Mary (Silent Hill 2) ... the list goes on and on!
That fight was a bitch and a half. :P Although, I prefer the game's TRUE final fight. Although it was actually painfully easy once you figured out the trick (hitting the pause button, counting the rings, unpausing and jamming out the appropriate two or so presses, pause, and so on). Still, it gets major points just for being the freakiest thing in the whole game (and let's face it, Drakengard's mind-effery comes just shy of Silent Hill).
Also, not sure why I didn't mention it earlier, but (SPOILER)Zophar from Lunar 2 was an incredible "final" encounter. Not only was he disgustingly challenging, but he gets extra points for being probably the only "ancient evil" in the entire genre to actually freak me out on a regular basis. If you're going to make a villain that is nothing more than the embodiment of all evil, then at least make me feel it the way Lunar 2 did. I still have nightmares.
Currently playing: Metal Gear Solid: Peace Walker
I love Xemnas and Bhaal from Kingdom Hearts II and Grandia, respectvely.