Subarachnoid Space is a must. Very trippy, Floyd-esque space prog rock.
As mentioned before, Ayreon, specifically the album "The Universal Migrator" (both parts)
Mortiis' "The Smell Of Rain" is his later, more techno-influenced work and thus has a more sci-fi feel to it. There's also "The Stargate" and a side project called Fata Morgana that are EXCELLENT ambient albums, but they tend towards more of a fantasy theme rather than sci-fi.
Apoptygma Berzerk, almost any material really, though it might be not ideal since it isn't as strictly instrumental/progressive as most of the artists mentioned so far.
Kid606's "Resilience" and Squarepusher's "Hello Everything", tricky and trippy electronic music that jumble a crapload of different genres into the spans of single albums.
Oooh, almost forgot Arcturus! Their latest release "Sideshow Symphonies" about space pirates and contains some very effective metal music. Their back catalogue is also excellent, but the further back you go the harsher and more black metal their sound becomes.
That's as far as my brain can take me at this point.