My list is pretty close to David's.
1. Children of Men
2. The Fountain
3. Pan's Labyrinth
4. Babel
5. Good Shepherd
For me, Children of Men was hands down the best cinematography of the year. The next couple of pictures, for me, aren't that close. The Fountain was my #1 picture of the year, but cinematography was actually not its strongest element. The acting, music, and stunning macro-photography FX are just incredible in The Fountain, but several of the early jungle night scenes looked overlit to me. The "bathtub" scene in The Fountain, though, was perfectly shot and was the best stand-alone scene from any movie last year, IMO. Pan's was just flat out gorgeously shot, but I don't think its photography was as innovative or compelling as CoM's. CoM's photography is 100% vital to its storytelling -- to its very existence as a film. Babel was obviously another beautiful piece of cinema photography. The deserts of Morocco and the urban jungles and landscapes of Tokyo were my favorites locales. And the Good Shepherd was probably the most overlooked, because its photography was so perfect that it almost goes unnoticed. The photography was super professional, and never drew attention to itself.
I have not seen Marie Antoinette yet, but I suspect I am really going to like it. I'm hoping to see it in HD.
The biggest disappointment for me was Apocalypto, which I thought was going to be my favorite cinematography of the year, going off the trailer. I was also really excited because it was shot on the Genesis. But in the end, it only turned out to above average in cinematography. I'm not sure if it was Semler, or the camera, but it never lived up to my hopes.