Adaptation (2002)
Spring, Summer, Fall, Winter… And Spring (2003)
There are a few more that I thought were very good, but I'm not sure if I'd put them into my very top list
A History of Violence
AI
The Man who Wasn't There
United 93
Children of Men
Dark Knight
There Will be Blood
There are a bunch more, like Oldboy or City of God, that were surely brilliant but I haven't seen all the way through. The more I think about it, the more I feel this has been a pretty good film decade.