I'm thinking about posting below, and also updating this first post with stuff about 2013 films. Hopefully it'll give a good rundown at EOY time. Hopefully caley will do the same.
Iron Man 3: Unabashed love for this. I remember when Shane Black said that one of their goals was to go back to the roots, and make it more of a mystery, and less suit. Those scenes were really just as thrilling, if not more, than a bunch of stuff flying around the screen blowing up.
Oblivion: A good looking sci-fi film that is also just this huge mash-up of other sci-fi films. Some thrilling scenes, and some fairly well-kept secrets puts it in a category I'm not sure about. Both much better and much worse than a lot of similar big-budget films.
The Place Beyond The Pines: This movie REALLY surprised me. I had read a couple synopsis's that were a paragraph or two and was very surprised that it only covered the first 50 minutes of the movie or so. At that point the next 50 minutes is completely different, and the last half hour takes place 15 minutes later. It's honestly almost epic in scope.
The Pool: This film has a VERY limited run in 2008. FINALLY showing up on DVD. This thing won a jury prize at Sundance. It's directed by Chris Smith (American Movie, Yes Men), but it's a quiet narrative about human interaction. It takes place in India/is in Hindi.
Promised Land: Seemed to have an OK release in 2012, but no one voted for it, so I'm not sure if anyone saw it. I thought this was going to be a typical hippie save the world movie (this time about fracking), but it actually had some really interesting twists and turns.
Robot and Frank: Another Sundance film. Frank Langella is great as an old retired man whose son gives him a robot to keep in company. (Too bad the "robot's are going to take over the world" thread is gone.)
Room 237: An absolutely fascinating look at a handful of people's intricate theories on the secret meanings behind Stanley Kubrick's The Shining. I'm not sure if these people are insane or brilliant. Or both.
Samsara: My favorite movie I saw in 2012, this had a limited run in 2012 and came out on DVD at the very beginning of 2013. It's from the director of Baraka. RIYL: Koyaanisquatsi. I liked it better than both.
Side Effect: Was very surprised by this one. I thought it was going to be a pretty straight-forward drama, but there were some REALLY interesting plot twists that, while I saw them coming, I only saw them coming 5 minutes early, not 45 minutes early.
Upstream Color: Shane Caruth's (Primer) 2nd film is actually a lot easier to understand than his first film. While its structure may seem difficult at first, when the film was over we realized that we understood everything that was happen as the movie was going. This and Room 237 are the movies I saw this year that have stayed in my mind the most.
Warm Bodies: I enjoyed this zom-rom-com a lot. It's funny, not completely stupid and the characters are very likable.