If we can count a puzzle as the final boss, then the last puzzle in 999: 9 Hours, 9 Persons, 9 Doors. I was bawling while I was solving it, and it was the first time I cried while playing a video game. If you played it, you probably know why.

If it has to be an actual enemy... I don't think I have a definitive favorite, but I liked Quadraxis from Metroid Prime 2, Goht from Zelda: Majora's Mask, and Jubileus from Bayonetta among a number of others.

Yah definitely. That last puzzle in 999 made things really tense and depressing.

The Boss from MGS3 and Metroid Prime being a close second.

The Valkirya in Valkyria Chronicles was pretty cool.

Oh, I want to change mine to the Boss woman in MGS3 and also that crazy sniper elder. Also, all MGS3 bosses.

MGS3's bosses were the best though :P

Zanza IN MOTHA FUCKIN SPACE!!!!! Xenoblade Chronicles

Salazar - Resident Evil 4
Del Lago - Resident Evil 4
Gruntilda - Banjo Kazooie
Gruntilda - Banjo Tooie
Great Commander - Starfox SNES
Phantron - Starfox SNES
Ridley - Metroid Prime
Volvagia - Ocarina of Time
Ganondorf - Twilight Princess
Koloktos - Skyward Sword

Might want to censor that whole thing. 

I was having a hard time thinking of a good answer, but thanks to your post I thought of a really great one.

Ornstein and Smough from Dark Souls. Without a summon!