The first thing to say about this list is that because of my nature, my favorite 100 movies from 2000 through 2009 are culled from viewing that would under no definition be considered comprehensive.
How little do I see? Of 45 Best Picture nominees so far this decade, I've taken in 31. So I've missed nearly a third, including winners Gladiator and Million Dollar Baby. (The other nominees I've so far skipped: Atonement, The Aviator, Chocolat, The Curious Case of Benjamin Button, Finding Neverland, Frost/Nixon, Gangs of New York, Juno, Letters from Iwo Jima, Little Miss Sunshine, The Reader, and Seabiscuit. For something drawn from broader experience, look at Mike Schulz's list.)
It is certainly possible that some of these movies, if seen, would be on this list. Based on what I know about myself and these movies, though, there's a far greater likelihood that bypassing them was a sound choice. That's a sign of a less-than-fully-open mind, certainly, but it's also a matter of priorities: Do I think this movie would reward my time investment as much as [a different movie, sleeping, Wii, etc.]?
My 100 favorite movies of the decade follow, with links going to essays written for CultureSnob.net. After that are discussions about five filmmakers with multiple movies on this list.
The Top 10
2. Pan's Labyrinth
3. Requiem for a Dream
5. The Royal Tenenbaums
6. No Country for Old Men
7. The Mothman Prophecies
8. Mulholland Drive
9. Donnie Darko (original theatrical version)
10. The Descent (international version)