While it is true that 3D has been largely either "poke you in the eye" or "show it in 3D, even though the director refuses to acknowledge it", there are SOME examples to the contrary. The main one that stood out was Coraline, which I made a point of seeing recently. The director, in an interview, confirmed how I took his approach to be:
"There was a learning process – mainly not to overuse it. We ultimately used it to help draw the audience into the Other world as Coraline is being drawn into the Other world. The sets in the Other world are actually deeper. In her real world, it’s crushed space with steeply raked floors. For example, the kitchen in her real world is one foot deep. The kitchen in the Other world is four feet deep. I wanted to use 3D in a more subtle way to show what Coraline is going through, that there’s a sense of spaciousness in that Other world. We have a few shots where things poke you in the eye, but when the Other world goes wrong, we crank up the 3D almost to an uncomfortable level to enhance the storytelling."
Great usage of 3D in my book. It's too bad not many good directors are taking 3D seriously.