There's still a good deal of stuff I haven't seen, including The Road and Fantastic Mr Fox, but these are my top 5 from what I have seen:
5. The Informant!
4. Tyson
3. The Hurt Locker
2. Moon
1. A Serious Man
Also, big ups to Gomorra, Coraline, and Soderbergh's Che movies, which I can't remember if they came out in early 2009 or late 2008, but didn't open in my town until 2009, so I count them in the 2009 grey area. (I know, if only there were an easy way to find out what the release dates of movies were...)
Also, worst film that I saw theatrically in 2009: The Informers, hands down. And that's despite the copious nudity and Brad Renfro's fantastic, amazingly creepy performance.