Gosh there are just so many of them! Well if you say final bosses of first party Nintendo games. My top 3 would be (not counting Ganon twice).
Ganondorf - Wind Waker and/or Twilight Princess
Dark Samus - Metroid Prime 3 (Dat checkpoint tho)
Nightmare - Links Awakening
I want to give honorable mentions to Onox and Veran. The Zelda final bosses are often very well designed. Demise was really a let down in this aspect.