Probably Ganon in Ocarina of Time. Not the most amazing gameplay-wise but the overall experience is my favorite. Mother Brain in Super Metroid is a close second though.

Both of the Super Mario World games and SM3D World also have epic final battles.

Either the final boss from Super Metroid or Fire Emblem Awakening.

King K. Rool from DKC, that music and that feeling when he came back when I was congratulating myself... Good old times.

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.

There are so many greats, but if I had to choose just one, it would have to be giant baby Bowser from Yoshi's Island.

It's just so freaking epic. From the badass music, to the sheer scale, to how technically impressive it was for the time. (I like to see it as marking the transition to 3D that would come to fruition the following year in Mario 64)

Honorables mentions go to DJ Octavio and Metroid Prime.

Mother Brain 

Splatoon. What a great boss that was.

Canon from Ocarina of Time. The buildup to the fight was epic and the fight itself even more so.

Satoru Iwata

Bowser, Super Mario Galaxy 2