Babylon 5, Firefly, and (new) Battlestar Galactica are my top three favorite sci-fi shows. I've enjoyed others, from the Star Treks to (new) Doctor Who, but those three stand above the others I've seen.
Buffy & Angel are good'uns too.
Never been as big a fan of comedy shows, but Futurama is definitely up there for me. (Gee, sci-fi everywhere with me. )
I do keep hearing good things about Dexter. It sounds a bit much even for me, but I guess I'll have to watch it one of these days.