It was Prometheus for me. I've heard a lot people say "meh" about it, and I just don't understand that response. The movie was atmospheric, creepy, and just so sci-fi at the same time. They don't make movies like this anymore. It wasn't trying to be stylish, slick, or pander to certain audience. It was simply trying to tell us a good science fiction story, and I felt it did the job quite well. It had the feel of one of the original Trilogy Alien movies, which I loved.
I agree with you on Prometheus. I really loved it for the story and the questions it posed afterwards.
However, I went with the Dark Knight Rises. It was epic in so many ways, tied the trilogy up very nicely (I thought), and was just an overall great movie from start to finish. Avengers was a lot of fun, absolutely, and a great movie. TDKR just gave me the drama and tension and emotion that I wanted from it.