There have been some great sci-fi inspired music videos on youtube. Here are a few of my favourites:
Bohemian Matrix by icemancocker
Aliens Rap, from Robomayhem's page.
Total Recal: the Musical, from legolamb's page.
An older, but still amazing, video the Star Wars (John Williams is the Man) a cappella medley by Corey Vidal and Moosebutter
Weird Al Yankovic comes up with some great songs, The Saga Begins, about Star Wars Episode One is no exception. Taken from b2ftube's youtube page.
And a really old one, Star Trekkin' by the Firm. I heard this for the first time about 2 years ago, but it definitely deserves a newer audience. Taken from roopert's youtube page.