Only 10 minutes into the commentary for the Avengers and it's already impressive. Joss Whedon is talking about how he went about shooting 3D and he talks about how he didn't want to shove stuff in peoples' face, but rather that he wanted to use it to give a scope of the space and size of everything. It's an interesting and brilliant take on it. If more people had that take on 3D, I think I may like it better.
Using 3D to shoot bullets at the audience is gimmick. Using it to give us a sense of depth and size adds something that has always been lost in film.