as an huge scifi geek, my favorite shows are basically the following:
Battle-star galactica (both old and re-imagined)
Lexx (it was stupid at times but it had a certain charm to it)
Hitchhiker's guide to the galaxy.
Star Wars is my absolute favorite fictional universe! I fell in love with the series when I was only 5. The first time I saw Star Wars on VHS on a spring morning, I had to watch it again. And again. And again! I watched it five times that day! My parents were concerned. :p
My 2nd favorite sci-fi universe outside of Star Trek would be Macross. Do you all remember Robotech from the 1980s? Macross was the first Robotech series, which originally came from Japan. I don't consider myself a big fan of anime, but it's favorite piece of modern fiction from Japan!
it's a tough call but I really enjoy the following;
Firefly (they should at least make another couple movies to follow Serenity)
Terminator (Movies and short lived series)
Stargate (Movie and all following series)
BSG (old and new)
V (old and new)
Ender's Game (book series by Orson Scott Card)
There's more where that came from, but I'll leave it at that.