This was the top 50 (of 100) in the poll I mentioned. I'll post my list later.
50. Rois et reine / Kings and Queen (Arnaud Desplechin, 2004)
49. Munich (Steven Spielberg, 2005)
48. Collateral (Michael Mann, 2004)
47. Far from Heaven (Todd Haynes, 2002)
46. Code inconnu / Code Unknown (Michael Haneke, 2000)
45. When the Levees Broke: A Requiem in Four Acts (Spike Lee, 2006)
44. Incredibles, The (Brad Bird, 2004)
43. Paranoid Park (Gus Van Sant, 2007)
42. Adaptation. (Spike Jonze, 2002)
41. Requiem for a Dream (Darren Aronofsky, 2000)
40. Life Aquatic with Steve Zissou, The (Wes Anderson, 2004)
39. All the Real Girls (David Gordon Green, 2003)
38. Lord of the Rings: The Two Towers, The (Peter Jackson, 2002)
37. Squid and the Whale, The (Noah Baumbach, 2005)
36. Borat: Cultural Learnings of America for Make Benefit Glorious Nation of Kazakhstan (Larry Charles, 2006)
35. Million Dollar Baby (Clint Eastwood, 2004)
34. Ghost World (Terry Zwigoff, 2001)
33. Burn After Reading (Ethan Coen, Joel Coen, 2008)
32. Kaïro / Pulse (Kiyoshi Kurosawa, 2001)
31. Punch-Drunk Love (Paul Thomas Anderson, 2002)
30. You Can Count on Me (Kenneth Lonergan, 2000)
29. Departed, The (Martin Scorsese, 2006)
28. Sideways (Alexander Payne, 2004)
27. Ratatouille (Brad Bird, 2007)
26. Dogville (Lars von Trier, 2003)
25. Children of Men (Alfonso Cuarón, 2006)
24. Memento (Christopher Nolan, 2000)
23. Elephant (Gus Van Sant, 2003)
22. Artificial Intelligence: AI (Steven Spielberg, 2001)
21. Habla con ella / Talk to Her (Pedro Almodóvar, 2002)
20. Wrestler, The (Darren Aronofsky, 2008)
19. Lord of the Rings: The Fellowship of the Ring, The (Peter Jackson, 2001)
18. Laberinto del Fauno, El / Pan|s Labyrinth (Guillermo del Toro, 2006)
17. Lord of the Rings: The Return of the King, The (Peter Jackson, 2003)
16. Kill Bill: Vol. 2 (Quentin Tarantino, 2004)
15. Kill Bill: Vol. 1 (Quentin Tarantino, 2003)
14. Lost in Translation (Sofia Coppola, 2003)
13. INLAND EMPIRE (David Lynch, 2006)
12. Royal Tenenbaums, The (Wes Anderson, 2001)
11. 25th Hour (Spike Lee, 2002)
10. New World, The (Terrence Malick, 2005)
9. Before Sunset (Richard Linklater, 2004)
8. Fa yeung nin wa / In the Mood For Love (Wong Kar-Wai, 2000)
7. WALL•E (Andrew Stanton, 2008)
6. There Will Be Blood (Paul Thomas Anderson, 2007)
5. Zodiac (David Fincher, 2007)
4. Sen to Chihiro no kamikakushi / Spirited Away (Hayao Miyazaki, 2001)
3. Eternal Sunshine of the Spotless Mind (Michel Gondry, 2004)
2. No Country for Old Men (Joel & Ethan Coen, 2007)
1. Mulholland Dr. (David Lynch, 2001)