Koloktos - Zelda Skyward Sword - It's hard to choose a single Zelda boss.
15th colossus - Shadow of the Colossus - Really hard to choose a single one, too.
Riku - Kingdom Hearts
Magus - Chrono Trigger
Gobblegut - Super Mario Galaxy 2
Cynthia - Pokemon Platinum
Kefka - Final Fantasy VI - I was super overleveled when I battled him but it still was a great battle.
Vergil last battle - Devil may Cry 3