Since I started this I thought I would add a few thoughts about why each of these choices is on my list.
Andromeda: Not the best Roddenberry idea but better than at least two of the Star Trek franchise shows with good acting and compelling characters, especially the high guard ship.
Battlestar Galactica (original): Corny but entertaining, compelling story line, likeable characters, nice space hardware and dramatic (if repetitive) space combat; I loved Dirk Benedict as Starbuck and Richard Hatch as Apollo.
Battlestar Galactica (new): Fine cast and acting, compelling story plots, a darker tone than the original and surprising twists and turns in almost every episode.
Babylon 5: The best yet if I had to pick one; compelling action and drama, excellent cast and fantastic writing; the first to feature believable and interesting aliens.
Doctor Who: Great imagination and certainly entertaining, especially for its budget.
Doctor Who (2005): Really an updated version which is notable to me mostly for the new doctors (and Billie, of course).
Farscape: The sets, costumes, FX and co-star Claudia Black are all absolutely stunning; certainly rates in my top five.
Firefly: My second all time favorite; lower on Sci Fi and notable mostly for its superb cast and acting and excellent writing and character development set in a space setting.
The Invaders: A bit of the Fugitive pursued by aliens but quite entertaining mostly, especially for its time; with hindsight I might have better included V, especially the mini series.
The Outer Limits: "There is nothing wrong with your television. Do not attempt to adjust the picture"; a superb (especially for the time) episodic view of space and time travel; far ahead of its time and the source of material for many later series and movies.
Stargate SG-1: Good premise and fine cast but I frankly preferred the movie.
Stargate - Atlantis: A new variation that I have yet to sample but certainly has its legions of fans.
Star Trek (Original Series): The one that brought Sci Fi to the mainstream and interestingly tackled some then touchy social issues; Shatner and Nimoy were excellent together; if not for this show, many of the later Sci Fi series would never have happened; a must inclusion in the top 5.
Star Trek - The Next Generation: Excellent cast and interesting stories; likely the best of the franchise.
Star Trek - Deep Space Nine: Started weak and improved later; interesting stories and some good acting; many good episodes but overall I would rate it 4th in the franchise.
Star Trek - Voyager: The weakest of the franchise to me; of course it is saved by 7 of 9.
Star Trek - Enterprise: A close second to STNG for my favorite of the franchise. Very solid acting and interesting, if somewhat limited story lines. No question the writing for STNG was better but who could not enjoy Jolene Blalock (and her uniforms)?
Space 1999: One of the first interesting near future space adventures, decent acting by Landau and Bain.
Torchwood: Quirky but engaging, mostly earthbound so I probably should have left it out here.
For those that mentioned the X-Files, Nightstalker and Buffy, again, I was shooting for a more extraterrestrial focus.
Some reluctantly excluded were:
