My favourite is easy; Firefly. Then Farscape (Yay! Insanity! EDIT: Also, my home. I teared up a little because I was feeling very homesick when I watched it).
It's just after that putting them in order gets a little harder. That said, honorable mentions go to Battlestar Galactica (One of the few Sci-Fi series which ended before being canceled) and Stargate: Atlantis (because it managed to keep the fun and adventure from SG:1, that SG:U couldn't, with better production)
Also; I usually use threads like these as a way of discovering new shows. So for anyone who does the same, here's some other Sci-Fi which are, at the very least, interesting.
Caprica - I actually feel like putting this with the honorable mentions, but I've got to no idea why. So it's here. It's a spin-off of Battlestar Galactica, so if you like one watch the other.
Dark Angel - Hit and miss. It had a relatively interesting setting and premise, but the writing wasn't consistent. First season was impressive, second season was painful.
Stargate: SG-1 - It takes awhile for it to find it's feet, but if you can get over that hump it's just fun.
Stargate: Universe - It feels more like Battlestar Galactica than it does Stargate, but it's not bad. It takes itself too seriously though.
Fringe - Worth watching just because of Walter Bishop. Seriously.