Hands down, I think the best science fiction music videos I've seen are those of Daft Punk's Discovery album (released March 13, 2001). They presented their album to anime creater Leiji Matsumoto, and each track was made into an episode for the movie Interstella 5555: The 5tory of the 5ecret 5tar 5ystem (released Dec. 1, 2003).
The film doesn't have any dialogue but rather tells a story of blue humanoid alien musicians who are kidnapped, taken to Earth and made to look like humans. Their memories are rewritten, and they are made into a hit band on Earth called The Crescendolls. One of their kind later saves them from the human captors but dies in the process. Eventually, the world finds out that the band members are aliens and help them to return to their homeworld.
My favorite music videos are "Aerodynamic" (it's the second episode) and "Harder, Better, Faster, Stronger" (the fourth episode).
Daft Punk sampled several older songs by other artists to make tracks on the album. For instance, Edwin Birdsong's "Cola Bottle Baby" was sampled for "Harder, Better, Faster, Stronger," and, likewise, Daft Punk's version was sampled for Kanye West's song "Stronger" from the album Graduation. Daft Punk created the soundtrack to the movie Tron: Legacy.
What are your favorite science fiction music videos?