WoW, only two people mentioned Babylon 5 and nobody mentioned LEXX!
Those are my two fave Sci Fi shows.
Babylon 5 is a classic and seminal work because it was the brainchild of one person, not a team of script writers (yeah I know others wrote episodes, but it was the vision of one person). Why is that important, welp, in one of the episodes in the first season, Londo has a premonition of a shitload of bloody scary looking spaceships flying over his home planets capital city (Shadows) and this was long before we even knew what the Shadows were. In the fourth season we actually see his premonition come true!!!
The story arc was massive!!! You just don't see that sort of thing in sci fi anymore (or previously for that matter). JMS's vision was astounding! He developed characters that we still miss to this day and I can still watch episodes 10 years after they were originally shown with the same enthusiasm as when they first aired.
LEXX was written by three college buddies in Halifax, Nova Scotia (I've met these guys and they are nuts!). The first season is like watching a Hollywood epic written by talented graduates stoned on dope with HUGE budgets! The special effects were absolutely groundbreaking (done in Germany because Pixar and the other dude couldn't handle the computing power needed - and they were too expensive) and although there were a couple of render errors, the story, effects, sexy leading lady and total anti-hero (Stanley Tweedle) made me a fanatic about the show.
Although the production company fucked up in the last series (4), LEXX will always be the most groundbreaking (weird ass stuff) sci fi show - I honestly can't see anything getting as close.
Aeon Flux (animated series and Cowboy Bebop/Outlaw Star (which influenced Weddon to make Firefly) are also worth a mention and of course the Brit series Red Dwarf and Hitch Hikers Guide to the Galaxy are exceptional because they managed to make sci fi comedy - nobody has managed to do that since (sept 3rd Rock - which wasn't very good I don't think).
Whew. Bit of a rant that, but ..... well, you asked