For me its Hugo and Gravity
Life of Pi, hands down. I saw both those movies, and while they both featured some proper use of 3D, neither of those iterations of the technology added nearly as much to the cinematography as Life of Pi's, which had the most beautiful and inventive use of 3D I have ever seen in a movie theater.
This thread made me miss Screened.
I've never gotten on with 3D, to the point where I actually cobbled together a set of '2D' glasses from a Tested video so that I could get through a 3D film without a splitting headache and actually see what's going on. That said, the floating particles in Avatar (mainly the ash and the insects) were actually very immersive.
Seeing a 3D movie is like paying extra to watch a movie while wearing sunglasses. The colour gets washed out and the motion feels choppy when wearing those glasses. At best the 3D effect might be neat for the first 5 minutes of the film, but after that you no longer notice.
As for the best 3D movie? Coraline was the first movie I can recall where 3D was used to create depth instead of just having things pop out at the viewer.
I thought the 3D in Avatar was really cool and then for several years was hugely disappointed by pretty much every 3D movie I saw and felt with a lot of movies the 3D made it worse, but recently there have been a slew of movies that I've loved the 3D in and thought that it actually adds to the experience. The LEGO Movie, Gravity and Pacific Rim all immediately come to mind.
All of those times I watched movies and never realized it was 3D work. I have watched some behind the scenes stuff recently of a lot of different movies and the number of scenes that have 3D work that look realistic is mindblowing. 3D artists don't get enough recognition for their work.