Honorable Mentions, in no particular order:
The Twilight Zone, which is an enduring classic, with good reason.
The Outer Limits, which also had some really great episodes. More science-fictiony than Twilight Zone.
Dr. Who. Not what I'd call an entirely serious show, but I loved it growing up. Perhaps the greatest camp series in the history of TV.
Star Trek: The Next Generation. A show that had some very good moments despite its many problems, mostly uninteresting characters (the exceptions being Data and Worf,) and total lack of vision. It was generally well-acted but poorly-plotted, with far, far too many deus ex machina Geordi/Wesley technobabble plot resolutions. It's also a very important show for TV in general, since it helped develop much of the system of syndication that made it possible for shows like Hercules, Xena and Highlander to get aired. (The blame for Renegade and Kung Fu: The Legend Continues can also be laid at TNG's feet.) Nevertheless, as science fiction, its quality is comparable to
Alf. Its constant smarmy, pipe-to-the-head moralizing set my teeth on edge. (TOS was just as much a morality play, mind - but it usually worked as adventure and as drama better than TNG did, so it wasn't as ham-fisted, and you cared about the characters.)
Highlander: It's sci-fi if you accept the Planet Zeist storyline (There Is No Planet Zeist.)

It did have a few good moments, despite the show's formulaic nature and the producers' unwillingness to break away from the limited concept. The show works better if you see it as a continuity wholly separate from the movies.
My top Five:
5)
Farscape. Somewhat overrated, IMO, though it has its moments, and a very good developing storyline. Unusual for a sci-fi show in that it seems not to care too much about universe-building. It also, as far as I'm concerned, gave me little reason whatever to give a damn about the characters, except for Crichton, and he's a whiner.
4)
Star Trek: Deep Space 9. The best of the pseudo-Treks, and a good show in its own right. It at least had the good sense to
try to shake up the flat, stagnant Trek universe. "Trials and Tribble-ations" salvages much of modern Trek.
3)
Stargate SG-1. There's a been a backlash against it, I think, beacuse it's perceived as the show that bumped Farscape off Sci-Fi's lineup, but I consider it by far the superior show. I personally stayed away from it for years beacuse MacGyver's in it. SG-1 does an amazing job of developing and enlarging its core concept and of building a coherent and interesting universe around it. I'm convinced that it would be far more popular if it's hadn't spent its first several season on Showtime where nobody could watch it. The stories make sense, the pysics is consistent with itself, and the stories and acting are rock-solid. The best sci-fi on first-run TV right now, hands-down.
2)
Babylon 5. Yes, the acting is weak at times, but not everywhere - and in a few spots, B5's acting blows away
anything in any Trek. But it's
science fiction, not TV sci-fi, much closer to what we get out of the literary genre than out of television. The overplot is epic. B5 is the only TV show with scenes that give me chills (G'Kar's speech as he's being kicked out the the B5 Council at Londo's insistence... brrr.)
1)
Star Trek. There
is only one, and it ended in 1969. Everything since has been inferior pseudo-Trek.
I exclude my favorite genre show (Buffy) beacuse it isn't sci-fi. Shows that aren't on the list include Firefly (because I never saw it,) Space: Above and Beyond (a good show I don't think was on long enough to be a
great show,) Battlestar Galactica (for similar reasons,) Andromeda, Lost in Space, Enterprise, Voyager and the X-Files (beacuse they're garbage.)