My initial reaction was to proclaim my love of Avengers 3D over Avengers 2D (not for Scarlet Johanson's ass, you pervs) but then I realised I saw it in 3D Imax which makes the comparison totally irrelevant.
Speaking of 3D films in general, I basically agree with Matt. Avatar was, is, and I fear always will be, the epitome of a 3D movie. Simply for the fact that James Cameron understands what 3D is about. The idea of 3D is that I feel immersed, even wearing ridiculously stupid giant glasses I feel like at any moment I could reach out and stroke that tree. And he shot that entire movie to reflect that understanding.
The rest of Hollywood, however, appears to have one of two approaches to 3D. The first and most common: Here's a great 2D movie. Let's 3D it for more money. The second and, whilst amusing at first is just boring now: Well you know we have that one scene where this happens, if we film it like this it'll be like it's coming out at the audience.
Aka, 3D is just a cash cow or a gimmick. The first leaves you wishing you'd just paid to watch 2D instead, whereas the second gives you the same feeling with the added insult that you walk away feeling like the studio just had to flaunt its 3D tool in your face simply because it can.
That said, I find the in-your-face gimmick works well on animated movies. I have to say that I have yet to walk away disappointed from an animated 3D movie.