How about "Coraline"?
And "How to Train your Dragon"?
And "How to Train your Dragon"?
The only movie I've ever seen where 3D added something to the experience was an IMAX documentary about fish played in a ten-storey high screen. Combine the three-dimensionality with the peripheral-view-filling nature of the IMAX screen and you really have something. I think it might work better for documentaries than for narratives, though.