1. Children of Men
This is not only my favorite film of 2006, it is one of the best films I've seen in years. That statement might be a bit premature, as I've only seen the film once, but I plan to watch it again soon, and I am confident that it will live up to the claim. Alfonso Cuaron is one of my new favorite directors,. He's been getting better and better with each film. This film is by far his best, and the craft of his filmmaking is awe inspiring. I left the theater feeling like a kid again, blown away by the magic of this movie. I haven't felt that way in a long time.
2. Apocalypto
Not perfect, but some awe inspiring filmmaking. Mel Gibson takes you back to pre-columbian Mayan Central America, and it's as if you've stepped out of a time machine. Visually stunning. Inspired chase sequences. Probably some of the best production design you've ever seen in a film. Go see it in the theater before it ends it's theatrical run.
3. Pan's Labyrinth
I'm not a big fan of Guillermo Del Toro, but I was pleasantly surprised by this film. It's far from perfect (it's characters are shallow and oversimplified), but the world is fresh and imaginative, the film visually stunning, and the filmmaking top notch. It's "Spirited Away" for adults.
4. Thank you for smoking
Clever, witty and informative film. A very impressive first feature from Jason Reitman.
5. Borat: Cultural Learnings from America
Can't really say much for this film. It's just friggin' hilarious, and it's like nothing I've ever seen before.
Honorable Mentions: An Inconvenient Truth and Talladega Nights.
If you haven't seen any of these yet, go and check them out. If you're lucky, you'll still be able to catch some of them in the theaters.