I don't think anybody has even mentioned these yet, but I really like the Melnorme and Slylandro (not the probe) themes.

Other favorites include the Vux, Starbase Commander, Yehat, and Spathi themes. But you know, I can't think of even one that I *don't* like. The music for this game was excellent, just like every other aspect. I can't wait for the port to be finished so I can play it again. =)