Farscape
Fringe
I cannot recommend Babylon 5 enough, it is some of the best science fiction I've ever seen
Falling Skies
All of these have been listed already, but they're worth checking out, especially Babylon 5.
Also, these may be harder to track down, but Steven Spielberg's Taken mini-series was pretty good, and even harder to track down are two science fiction series on Fox back in the 90s:
1. Space: Above & Beyond (About mankind's first contact and subsequent war with extraterrestrials in the late 21st century)
2. The Visitor (WW2 pilot ends up back on Earth, trying to do good deeds as he and humanity are being judged by the aliens who abducted him)
I'd also recommend both the classic and the remake of Outer Limits. It's hit or miss, but some episodes were very good.
There's also Psi Factor: Chronicles of the Paranormal, a good Canadian series from the late 90s. Not every episode is sci fi, I'd say, but they try to keep things grounded in science.
Andromeda and Earth: Final Conflict are worth a look as well.