The only modern 3D film I've seen is Avatar and I really liked it. I thought what Cameron did, not making the 3D aspects intrusive or blatant, was excellent. He used it to his advantage, but didn't throw stuff at you just to prove he could.
On the other hand, the trailer for the new Alice in Wonderland film (which isn't even broadcast in 3D) looks like they have stuff in there just because it'll look cool in 3D. Not a fan of that.
In Avatar, a whole new world was created and 3D helped to suck you in and make you feel a part of it. Even though there were real world components to it, the alien look set it off on it's own. Every day we walk through the "3D" real world of buildings and cars, you don't need to make a film set in reality 3D to tell a good story. Spider-Man, for example, doesn't need to be in 3D just so the director can try to wow us with a web shooting at us or Spider-Man swinging out of the screen. It's just use of technology for the sake of using technology.
It's like every commercial using bullet time after the Matrix came out, just because they could. Now it's just a gimmick to the point of being mocked in films as often as it's used constructively. Unfortunately, it's looking as if 3D will be the new gimmick for this decade.