SotC of course, and I will specifically choose the last boos fight because it was so long and epic. Hell, I think most of my favorite boss fights are because they took a long time and made me actually work hard to kill them.

SotC: no. 16
MGS3: The End

My boss was like ,"Lewis! You keep coming to work late and I'm going to have to fire you!!" And I replied, "Yes sir. It won't happen again". Epic.

Also, facing off with The End in Metal Gear Solid 3 or Gannon in Legend of Zelda TP was pretty awesome too!

No Capcom love from anyone but myself?

The two witches in OoT, hilarious scen after you beat them.

And Ganon in OoT, not Ganondorf but GANON

@Riot of Blood i wrote DMC 3 Vergil no.3

I loved the boss fights in metroid prime, except the last one, i hated it that much that i never completed this wonderful game.

the best were omega pirate and meta ripley because they were very hard.

it felt wonderful when i beat them

Zeus Boss fight for sure...perseus boss fight was pretty satisfying too

Pre-nerf Illidan in Black Temple from World of Warcraft, was one of the flame tanks, paladins ftw. good thing I quit WoW though.

some classics
Death Adder from Golden Axe
Mr X in Kung Fu
Cleopatra in Double Dragon 3
Shiva in Bare Knucle 3 (streets of rage 3)

Bah, there's too many. :p
Wizpig was epic. So was Ganon in OoT. Loved the Nightmare in Link's Awakening too. Well basically the Zelda series has tons of truly memorable boss fights, too many to name.
And Gruntilda in the original Banjo-Kazooie, and that Alien from Conker's. Twinrova was sweet, yes. And who can forget Bowser in SM64. :) Ummm, Metroid Prime! And Henry from NMH was awesome! Actually, pretty much all bosses from NMH were awesome! Aaaaaaand... Barbaros from Z&W. Okami had some great boss fights as well, though having to beat Orochi 19 times got pretty old. Oh, oh oh, and... ANDROSS!! Hell yeah! From Starfox 64, of course, the others were sucky. :p