[Picture of Carnivale title]
Oh, we're just generally recommending shows now? Alright.
I'd actually second Carnivale, but with the caveat that it's a weird mythology-driven series, some kind of supernatural apocalypse set in the 1930s, America, during the Dustbowl. The series was cancelled so the ending is unsatisfying, but the mythology was actually quite well thought out, which is refreshing.
It's definitely not for everyone though. A tl;dr description would be HBO's answer to Twin Peaks, which, given the casting of Michael J. Anderson in a prominent role, is sort of obvious.
No love for nuBSG? It's worth a look!
The new Battlestar Galactica is a fantastic series. In fact, being a dark, serious space opera with a serialized storytelling and morally compromised leads, it's more a 21st century heir to Deep Space Nine and Babylon 5 than any other TV show. Sure, the series can get frustrating, and the mythology arc is less satisfying the more you think about it, but in many other respects - its approach to drama, characterisation, the political and military content - it's one of the best space operas around.
[yt]http://www.youtube.com/watch?v=DgCwuWaVXdA[/yt]
My own recommendations would be kind of scanty, as I can almost name the sci-fi shows I actually like from the last decade on one hand. But what it's worth, if you want a cool, weird sci-fi show that blends a tale of interlocking alternate realities with ecological concerns, cyberpunk, and a fresh South African setting... there's always Charlie Jade.
[yt]http://www.youtube.com/watch?v=etRMoD2034o[/yt]
Or go find Dr Who, obviously.
Never cared much for Who.