Here's a list I have maintained and updated for over a decade.
Best live-action SF (not fantasy)TV shows of all time:
1. STNG- Still the best combination of all the elements that make ST great. It maintained the much of the topicality of TOS while adding more sophisticated drama and technical superiority.
2. TOS- Possibly packed more allegory into it's stories than any other SF show in history. This show is a classic because of stories that can be watched repeatedly with the viewer coming away with something each time. The best paced, most adventurous ST show of all. Only the third season keeps this one from ranking first. Re-mastered editon helps this show keep pace with other SF that has followed the original, and made it even better!
3. Twilight Zone- TOS's greatest competition as a show with deeper meaning, though it was not strictly SF. The acting is terrific, atmosphere eerie, and stories top notch. Serling is one of the greatest teleplay writers that ever lived, and the dialogue is dense and satisfying for multiple viewings.
4. Outer Limits- The purest SF show in history. Explored scientific extrapolation in a very mature way for it's time and medium, and it always showed the advancement as it related to humanity. Actually more mature in it's scientific view than the new OL.
5. STDS9- The black sheep of the ST family, but also the most complex dramatically and politically. Only scattershot comedies, a mediocre 2nd season, and a somewhat disappointing final season keep this one from ranking higher. Best seasons: 4-6...as good a 3 year span as ANY show.
6. Lost-While not as spellbinding as early seasons, this maddening show has become even more SF themed in later seasons, and I really still want to know what's going on!
7. Heroes-Engrossing first season and I probably would have ranked it ahead of Lost at that point. Still a good show.
8. Hitchhiker's Guide to the Galaxy- While not nearly as good as the book, this still has enough satirical laughs for a dozen regular TV shows. Everyone should aee this at least once.
9. Twilight Zone(1980s)- This show lacked the same consistent human commentary of the first, but contained so many excellent episodes I have to rank it here. Won numerous industry and genre creative awards.
10. New Outer Limits(1990s)- More paranoiac cautionary tales than the first show, but also great acting, clever episodes about contemporary scientific advances, and episodes with a lot of emotional impact. The 2nd best SF show that began life in the 90s.
11. Doctor Who(2005+)- I fun romp punctuated with some dark moments that continues the best traditions of the original, imperfect series and melds it with 21st century sensibilities.
12. Babylon 5- Instant mythology and good intentions but imperfect execution. Still one of the better attempts at space opera ever.
13. Battlestar Galactica (2003+)-Mainly on the strength of its first 2 seasons and its contribution to the genre on TV the last few years.
14. Star Cops- A mature, intelligent look at early 21st century policing of the newly emerging space race. Terrifically complex drama, and good FX for a BBC show.
15. Blake's 7- More than meets the eye. It is an adventure show but with a decidely un-Treklike bent--the heroes are criminals. Took the anti-hero to new heights in SF TV in the 70s.
16. Enterprise-A show that improved almost every year! Excellent production values and stellar 3rd and 4th seasons makes this one a winner and no doubt would have ranked higher with a 3rd season of momentum.
17. Max Headroom- Short-lived, and ahead of its time. It never quite fulfilled it's promise, but no show on American TV has ever been so unconventional. Some nice commentary on the media and it's impact on society.
EDIT: Oh I JUST read the website list after I posted this...um no...Logan's Run and Xena????
(But at least they put Moore's New Galatica as No. 1) 
. But yeah, having VOY but not DS9 seems very odd to me.
