I took the 3d plunge a while ago and use it once in a while. I have 3D Vision and an Asus 3D monitor. My personal favorite games in 3D are Trine 1 & 2 and Assetto Corsa. Trine is probably the best game I've ever played in 3D, if you don't have it you must get it. Assetto Corsa is a driving sim that is still in beta but with a Logitech G27 wheel and 3D Vision the game is pure bliss when driving a Ferrari 458 Italia around the track.
The problem with a lot of games is Nvidia never patches in 3D correctly so you have to use Helix Mod to fix them. Helix Mod is a god send and fixes most games and makes the 3D effect perfect or much better than Nvidia. I usually try a game in 3D at least once but a lot of them I just don't see the point. Eye strain can become an issue after a while especially if you max the 3D effect. I usually max the 3D and tone it down a bit but some games just look the best maxed out. I haven't had to many problems with performance with the rig I run. I7 2600k, 8 gig DDR3 and a 680GTX. Not the best anymore but it runs everything I throw at it still. Once Oculus Rift comes out 3D is going to be even better.