I couldn't choose a favorite, BEST SHOW EVAR any more than I could tell you which one of my children I love more. Different shows have different appeals.
Star Trek (ST:OS) - The first and arguably the best. It didn't define the genre (plenty of shows had already done some of what Trek had done), but it showed how good the genre could be. Instead of the 'monster of the week' format of Outer Limits, for example, it might feature an episode that was reminiscent of a Shakespeare play, or a comment on the nature of man's inhumanity to man.
ST:TNG - At first merely accepted by SciFi fans like a man in a desert accepts a glass of cold water, ST:TNG eventually threw off the shackles of bad writing and formulaic episodes to occasionally produce some brilliant episodes, and a lot of average ones. With a strong cast and a sizable budget, TNG had lots of highs and lows (it's dependence on a static environment, no inter-cast conflict or long term character growth being some of it's weaknesses). But this is made up for with episodes like "Darmok", "Brothers" or the one where Picard lives an entire life on an alien world.
Dr. Who - Not just a kids show, and the longest running sci-fi show EVAR. Quality varied wildly from incarnation to incarnation and season to season...but it featured excellent actors (from the RSC and stage as often as not), good humor and often very inventive plots. Not just the early Tom Baker seasons, but the whole run had amazing episodes. Go watch "The Pyramids of Mars" or "Talons of Weng Chiang" and remember what fun scifi is like.
Babylon 5 - If I had to choose just one show, this would probably be it. A testament to one man's desire to see a vision realized, come hell or high water. A show that holds together much better when seen in order, like the chapters of a book. More internally consistent than most shows could even dream of, B5 had a beginning, middle and end, and did it on a budget. While inconsistent (particularly during the first season), few shows have ever had the intensity of seasons 2-4 or carried the philosophical or emotional impact of their meta-stories.
Blake's 7 - A counterpoint to everything Dr. Who was. Not heroes, anti-heroes. Not comedy, black comedy and gallows humor. Working on a budget comparable with most BBC productions, B7 took risks within the genre, and had the best ending of almost any series, ever. We were left with our jaws on the floor when it was over.
Alien Nation - Odd that I haven't seen anyone toss out the mad propz to this highly underrated series. At first just appearing to be a poor follow-on to a cheap sf gimmick movie, it turned out to be an extremely well written show about the integration of an alien species with mankind, and the cultural conflicts that came with them. One reason for the show's success: R. O'Bannon...who's next series would be a little known show called:
Farscape - A show that took genre conventions and rotated them. With amazing visuals and quirky characters, Farscape knew it's audience had seen all the classic plots, like 'the body switch episode' or 'unstuck in time episode', and instead took them in radically different directions. (Favorite example: "You're trying to trick me...well I ain't buying it!' "Trick you? No, I'm just trying to drive you insane." Farscape's second take on the 'mind control/you've come home plot). Unpredictable and fast-paced, Farscape always seem to knowingly wink at the audience and say..."watch what we do, now".
There are others, of course, but these are the biggies.
