-Master Yonlach (SWTOR, Sith Warrior story), because you have to have fight 2 strong opponents with no companion, making it unreasonably unfair.
-Parasite Cage (Kingdom Hearts Chain of Memories, GBA), because wowzers, getting your combos broken by an unlimited supply of 0 cards with a floor that damages you is FUN MY LIFE
-Ashnard (FE9, Path of Radiance, the gamecube one with Ike), because my Ike got Strength-Screwed. D- Don't ask.
It's not a boss, but my personal Nemesis:
-The Sigil ennemies (Persona 4). My only 2 Game overs in P4 were due to those f*ckers, once in Void Quest, the second one in Heaven.