I really liked Avengers, but I think I prefer superhero movies with fewer main characters. I was very impressed, though, by how well the otherwise trite plot of the squabbling team that has to pull together.
The final Batman movie stands out to me. The sense of despair and then hope was amazing. I resisted seeing the second one for a long time, because the Joker seemed so intensely... real... for lack of a better word. I finally did see it, and am glad I did, because for all its darkness it was a necessary precursor to the final movie.
And, of course, there's the Incredibles, which I watch once a year or so. It's brilliant.
Finally, Mystery Men. There's some off-color humor moments, but for the most part the comedy is wonderfully odd and well done. Oh, and Scott Pilgrim vs. the World, which also has some questionable elements, but a lot of brilliance as well.