Theres a sci-fi reference in Fatboy Slim's Weapon of Choice. It's "Walk without rhythm and you won't attract the worm." I'm thinking it's a huge dune reference, but I guess I could be wrong.
That and Leonard Nimoy's Ballad of Bilbo Baggins.
EDIT: This is more Horror than Sci-Fi, but Gorillaz frequently uses samples from George Romero's Dead movies in their songs. (M1A1, and the intro to their new CD)
EDIT(2): System of a Down's I-E-A-I-A-I-O uses a riff from the Knight Rider theme, and the one line is "Former cop, undercover, just got shot, now recoverd" which is a reference to Michael Knights origins.