1. The Nameless One vs. The Transcendent One in Planescape: Torment, mostly for the incredible dialogue and the fact that selecting the text choices to avoid the battle actually gives you the cooler ending(s) IMO.
2. Darth Malak in KoTOR
3. Ganon in OoT (after the tower collapses)...I also really like the Phantom Ganondorf battle in the Forest Temple of that game.