I realize I already voted for 2D, but I think 3D has made leaps since I originally voted and I think there are many movies putting 3D to better use. So, I'd say, if a movie were designed for 3D in mind, right down to the cinematography, then I'd take it over 2D, but those are a few compared to those that are not. Avatar, Tintin, and Life of Pi are what I considered to have the best use of 3D.
Since I have a limited budget for going to the movies, I choose not to go to conversions. However, what I've noticed about theatres is they'll often squeeze out 2D, making 3D the only option. For example, when I finally got around to seeing Ironman 3, despite the fact that I didn't want to see it in 3D, I never had the choice, and the 3D wasn't very good in that.