Agree re Continuum, but my standout for original, funny, makes-you-use-your-brain recent scifi would be Fringe (tho it doesn't fit the 3 year bit). Top acting too.

Speaking of alternative realities, Awake was pretty good, and only one series, so doesn't need a huge time investment.

A personal fave at the moment is Arrow - best tv adaptation of a comic since the original Batman. Quite dark for a show that goes out at 8pm on sky!

And if you really like dark scifi, Utopia was excellent, in a seriously twisted way. Series two coming soon, I believe.

For pure entertainment Da Vinci's Demons was enjoyable, and I still have a soft spot for Supernatural.

And if you've not seen it - and again it's outside the 3 year limit - the Battlestar Galactica reboot was very good indeed.