Personally, I've never really been a fan of 3D movies. Generally too much 'OOOOh LOOK It's a 3D movie! Let's throw tons of crap at the camera and make the audience jump!'. For that reason I never liked them...
HOWEVER, I saw Star Trek Into Darkness in 3D and I have to say it was very well done. None of the stupid 'throw everything at the audience' garbage. Just added more depth to the movie. Didn't bother me at all.