Dark/Giga Bowser from SSBM is one of the finest final bosses in any game. Incredibly hard, impressive, has a good music, a cool arena... all the elements for a climatic final battle are there. Too bad SSBM didn't had the story to compliment its gameplay...
Metroid Prime in Metroid Prime 2 (if you havwe beaten the first game properly, then you know that Dark Samus is actually Metroid Prime in Samus's Phazon Suit). You don't expect that battle and it's an excellent proper final battle ; Emperor Ing is nothing to sneeze at but he has a little something... and the fact that he's Phazon infected is a big hint to the fact that he's not the true brain behind all your problems...
02 from Canvas Curse/Kirby 64. Best forms of the Dark Matter queen yet. The Kirby 64 form is the largest 02 form ever and one of the most impressive. The 02/Drawcia fusion at the end of Canvas Curse is also very interesting... although the fact that 02 and Drawcia separate during the boss's death animation might be a hint that 02 might appear in future Kirby games (like the upcoming one for Gamecube).
Andross is at his best in the SNES original game. Don't get me wrong ; I like his Starfox 64 form and his Starfox Adventures form isn't bad either... but its course 3 form in the SNES game has THE best second form you'll see in a Starfox game. Face it ; nothing beat a giant demon face of doom that fills the
screen REALLY quickly with spinning pannels.
Paper Mario 2's final bosses need mention. Two of the three, you expect them... the second one, however, is a surprise. Paper Mario 2 has probably one of the hardest final battles in a RPG game, period.
Menace from Dawn of Sorrow or Legion on steroids, if you prefer. Legion fusionned with human souls was already nasty... but when he gets merged with tons of demon souls on top of it, you get one heck of a big, bad boss! One of the best final battles in a Castlevania game yet.
Planet Meteo from Meteos. It's a big, gigantic eye that means business! Who doesn't like big eyes of doom and destruction?
Mewtwo from Puzzle League MUST be mentionned. He's one of the most nasty end bosses you'll ever see in a puzzle game, even maybe nastier than Meteo from Meteos (and that guy is already pretty crazy on "Brutally Hard"). Basically, you'll meet only if you're:
-Playing a no-save game and is Very/Super Hard
-Is properly playing the game (using a save slot) and thus, have obtained BOTH the Puzzle Key and the Champion Trophy and then, completed Very/Super Hard mode.
In both cases, Mewtwo's introduction is an actual cinematic. His speech isn't displayed on screen... he actually says it! In-battle, Mewtwo... well... is true to himself ; uber powerful. My only complaint would be that Mewtwo's defeat cinematic could have been longer and better but well... whatever, I guess.