Sorry to keep you all waiting! but I calculated that my list of favorite films of the 2000s wouldn't settle down until mid-2011 at least. And here we are.
I didn't try very hard to make this list a lot different from the 1999-2008 list that I posted amid the decade-end hurly-burly. But I allowed myself a few impulses that don't quite match my published lists of favorites.
1. Michael Clayton (Tony Gilroy, USA, 2007)
2. Esther Kahn (Arnaud Desplechin, France, 2000)
3. The Death of Mr. Lazarescu (Cristi Puiu, Romania, 2005)
4. Night and Day (Hong Sang-Soo, South Korea, 2008)
5. Vera Drake (Mike Leigh, UK, 2004)
6. Le doux amour des hommes (Jean-Paul Civeyrac, France, 2002)
7. The Child (Luc and Jean-Pierre Dardenne, Belgium/France, 2005)
8. Fat Girl (Catherine Breillat, France, 2001)
9. The Tracey Fragments (Bruce McDonald, Canada, 2007)
10. Raja (Jacques Doillon, France/Morocco, 2003)
11. Late Marriage (Dover Kosashvili, Israel/France, 2001)
12. Stella (Sylvie Verheyde, France, 2008)
13. The Sopranos: "Made in America" (David Chase, USA, 2007)
14. The House of Mirth (Terence Davies, UK/USA, 2000)
15. La face cachée de la lune (Robert Lepage, Canada, 2003)
16. The Son (Luc and Jean-Pierre Dardenne, Belgium, 2002)
17. Far from Heaven (Todd Haynes, USA, 2002)
18. The Forsaken Land (Vimukthi Jayasundara, Sri Lanka/France, 2005)
19. Ana and the Others (Celina Murga, Argentina, 2003)
20. Primer (Shane Carruth, USA, 2004)
21. Le Père de mes enfants (Mia Hansen-Løve, France, 2009)
22. The Exploding Girl (Bradley Rust Gray, USA, 2009)
23. Sita Sings the Blues (Nina Paley, USA, 2008)
24. Bled Number One (Rabah Ameur-Zaïmeche, Algeria/France, 2006)
25. Still Life (Jia Zhang-ke, China, 2006)
26. Ballast (Lance Hammer, USA, 2008)
27. Sangre (Amat Escalante, Mexico, 2005)
28. The Wayward Cloud (Tsai Ming-liang, Taiwan, 2005)
29. Silent Light (Carlos Reygadas, Mexico, 2007)
30. A Week Alone (Celina Murga, Argentina, 2008)
31. All Around Us (Ryosuke Hashiguchi, Japan, 2008)
32. Une Vieille Maîtresse (Catherine Breillat, France, 2007)
33. Japon (Carlos Reygadas, Mexico, 2002)
34. Waking Life (Richard Linklater, USA, 2001)
35. Bully (Larry Clark, USA, 2001)
36. Vibrator (Ryuichi Hiroki, Japan, 2003)
37. Crashing (Gary Walkow, USA, 2007)
38. Tout est pardonné (Mia Hansen-Løve, France, 2007)
39. Darling (Johan Kling, Sweden, 2007)
40. Eighteen (Jang Kun-jae, South Korea, 2009)
41. Triple Agent (Eric Rohmer, France, 2004)
42. Chopper (Andrew Dominic, Australia, 2000)
43. Platform (Jia Zhang Ke, China, 2000)
44. Zero Day (Ben Coccio, USA, 2003)
45. Happiness (Hur Jin-ho, South Korea, 2007)
46. Lady Chatterley (Pascale Ferran, France/Belgium, 2006)
47. La Donation (Bernard Émond, Canada, 2009)
48. Woman on the Beach (Hong Sang-soo, South Korea, 2006)
49. The Garden of Earthly Delights (Lech Majewski, UK/Italy/Poland, 2004)
50. Or (Mon Tresor) (Keren Yedaya, Israel, 2004)
51. Toutes ces belles promesses (Jean-Paul Civeyrac, France, 2003)
52. Ken Park (Larry Clark and Ed Lachman, USA, 2002)
53. Ten (Abbas Kiarostami, Iran, 2002)
54. Barbe Bleue (Catherine Breillat, France. 2009)
55. Jealousy Is My Middle Name (Park Chan-ok, South Korea, 2002)
56. Shara (Naomi Kawase, Japan, 2003)
57. The World (Jia Zhang-ke, China, 2004)
58. Roberto Succo (Cedric Kahn, France, 2001)
59. Îles flottantes (Nanouk Leopold, Netherlands, 2001)
60. Be My Star (Valeska Grisebach, Germany, 2001)
61. Face (Tsai Ming-Liang, France/Taiwan, 2009)
62. Avant que j'oublie (Jacques Nolot, France, 2007)
63. The Darjeeling Limited (Wes Anderson, USA, 2007)
64. Grain in Ear (Zhang Lu, China/South Korea, 2005)
65. Nights and Weekends (Joe Swanberg and Greta Gerwig, USA, 2008)
66. Mid-August Lunch (Gianni Di Gregorio, Italy, 2008)
67. Turning Gate (Hong Sang-soo, South Korea, 2002)
68. Wolfsbergen (Nanouk Leopold, Netherlands, 2007)
69. Jesus, You Know (Ulrich Seidl, Austria, 2003)
70. Morphia (Aleksei Balabanov, Russia, 2008)
71. Paris: XY (Zeka Laplaine, France, 2001)
72. The Believer (Henry Bean, USA, 2001)
73. All or Nothing (Mike Leigh, UK, 2002)
74. Crimson Gold (Jafar Panahi, Iran, 2003)
75. No Rest for the Brave (Alain Guiraudie, France, 2003)
76. Forty Shades of Blue (Ira Sachs, USA, 2005)
77. C.R.A.Z.Y. (Jean-Marc Vallée, Canada, 2005)
78. The King of Escape (Alain Guiraudie, France, 2009)
79. Rain Dogs (Ho Yuhang, Malaysia, 2006)
80. Catastrophe (David Mamet, Ireland, 2000)
81. The Virgin Stripped Bare by Her Bachelors (Hong Sang-Soo, South Korea, 2000)
82. She, a Chinese (Guo Xiaolu, UK/France/Germany, 2009)
83. Johanna (Kornel Mundruczó, Hungary, 2005)
84. A Tale of Cinema (Hong Sang-soo, South Korea, 2005)
85. Brick (Rian Johnson, USA, 2005)
86. Beat (Gary Walkow, USA, 2000)
87. Head-On (Fatih Akin, Germany/Turkey, 2004)
88. Boogie (Radu Muntean, Romania, 2008)
89. Hannah Takes the Stairs (Joe Swanberg, USA, 2007)
90. The Royal Tenenbaums (Wes Anderson, USA, 2001)
91. The Fluffer (Richard Glatzer and Wash West, USA, 2001)
92. To Die Like a Man (João Pedro Rodrigues, Portugal, 2009)
93. The Paper Will Be Blue (Radu Muntean, Romania, 2006)
94. The Banishment (Andrei Zyvagintsev, Russia, 2007)
95. Dog Days (Ulrich Seidl, Austria, 2001)
96. Harmful Insect (Akihiko Shiota, Japan, 2001)
97. The Days Between (Maria Speth, Germany, 2001)
98. Four Nights with Anna (Jerzy Skolimowski, Poland, 2008)
99. The Return (Andrei Zvyagintsev, Russia, 2003)
100. Cinema, Aspirin and Vultures (Marcelo Gomes, Brazil, 2005)