The stuff that everyone else hasn't mentioned already:
Alternity (the universe in TSR's sci-fi RPG system, also in novels based on it)
Gene Roddenberry's Andromeda, which obviously had a lot of problems but still had a universe with a lot of elements that I find interesting.

Apprentice Adept series by Piers Anthony (okay, so only marginally sci-fi, more fantasy

)
Otherworld (which was cancelled too soon)
V - including the series and all of the novels except the stupid "Second Generation" BS
ZORK, Enchanter, and the related Infocom universe - barely sci-fi in any way, mostly fantasy, but I love it so much that I'm mentioning it anyway.
The rest of my list:
Asimov's Robots/Empire/Foundation universe
BSG and nuBSG
Chalker's Four Lords of the Diamond, Quintara Marathon, and Rings of the Master series
Diane Duane's Star Trek - which I prefer to canonical Star Trek when it conflicts
Farscape
Firefly
Honor Harrington and the Honorverse
Knight Rider (TOS, 2000, and elements of the newer show)
Mass Effect
Quantum Leap
Star Wars
Stargate (all of it)
Transformers (G1 - including comics, Beast Wars, Beast Machines, and Prime only)
And I'm certain there are others that I will feel dumb for excluding later.