The Bespin duel's climax (beginning of Rescue from Cloud City, Hyperspace) made for some very evil atmosphere in Jedi Academy, too bad the game ended in Korriban which is nowhere as moody.
For some strange reason I'm also very fond of the Cloud City music, but more specifically the part that begins playing still in Dagobah (middle of Imperial Starfleet Deployed). One day I had begun the tenth level of Jedi Knight, right atop the Sulon Star with the cloudy sky flowing above me and it started playing. The impression has stuck with me ever since.