I think it depenRAB on the film to be honest..
Coraline and the recent Final Destination IMO both used the 3D really well, and made the film more interesting. (I hated the FD film though, but the 3D was well used..to be fair).
But when my cousin went to see Avatar in 3D with her boyfriend, it just annoyed them, it took their attention away from the film.
I haven't seen Toy Story in 3D yet, so I'll reserve judgement..but I'd imagine it'd be like Coraline, in terms of the 3D effect.