I've been happy with most 3D movies so far. I haven't seen Avatar at home because I refuse to pay over 60 bucks for it so that might be the best, I dunno. But from what I've seen, Alice In Wonderland. Even the Live-Action scenes (converted from what I understand) looked great. Some of the scenes that made me like "Hell yeah 3D is awesome" that come to mind are when she first gets into Wonderland and there's the rocking horse and the dragonfly fighting. It looks like they're fighting in my living room. The scene that I've seen with the most pop of all movies though is when Mad Hatter is fighting.. err.. the Queen's boyfriend-ish guy? When he blocks Hatter's swing it looks like the sword is sticking out like 2 feet from the TV.
I also thought the 3D was really well done in the IMAX sampler for Galapagos and Into the Deep. Not so much on Mummies. One of the coolest 3D scenes I remember in Galapagos was when the waves went over the lizard (don't remember what kind it was and I'm no biologist) and then back out to sea, the depth was awesome. And Into the Deep, when the camera was going through the Kelp Forests was really awesome, and it looked like fish were swimming around in my living room.
How To Train Your Dragon had some great 3D too. The scene that sticks out to me the most was when the big dragon at the end blew the fire onto all the Viking ships. Pretty much all the fire effects looked great in 3D though. In the scene where the big dragon and Toothless were fighting in the sky, when the big dragon blew fire all over the place it looked amazing, with all the different levels of depth from fire close to the screen to deep into the screen and everything in between.
I just realized I'm heading towards favorite 3D scenes in all of my movies so I'll go ahead and stop lol. Of the 10 movies I've got, those are the 3 I've thought had the best 3D