For the posts expanding on these choices:
Introduction #1-10 #11-20 #21-30 #31-40 #41-50
#51-60 #61-70 #71-80 #81-90 #91-100
See also: Honorable Mention, Other Worthwhile Films, The Worst of the Decade
1. In the Mood for Love (Wong, 2000)
2. Moolaadé (Sembene, 2004)
3. INLAND EMPIRE (Lynch, 2006)
4. Yi yi (Yang, 2000)
5. Mulholland Dr. (Lynch, 2001)
6. Grizzly Man (Herzog, 2005)
7. Moulin Rouge! (Luhrmann, 2001)
8. Werckmeister Harmonies (Tarr, 2000)
9. The Best of Youth (Giordana, 2003)
10. Talk to Her (Almodóvar, 2002)
11. Before Sunset (Linklater, 2004)
12. The Beaches of Agnès (Varda, 2008)
13. The Heart of the World (Maddin, 2000)
14. The Triplets of Belleville (Chomet, 2003)
15. The New World (Malick, 2005)
16. A.I. Artificial Intelligence (Spielberg, 2001)
17. WALL·E (Stanton, 2008)
18. The Fall (Tarsem, 2006)
19. Syndromes and a Century (Weereasethakul, 2006)
20. City of God (Meirelles, 2002)
21. Ratatouille (Bird, 2007)
22. Flight of the Red Balloon (Hou, 2007)
23. The Intruder (Denis, 2004)
24. You, the Living (Andersson, 2007)
25. In the Loop (Iannucci, 2009)
26. Goodbye, Dragon Inn (Tsai, 2003)
27. A Serious Man (Coen Brothers, 2009)
28. Flags of Our Fathers/Letters from Iwo Jima (Eastwood, 2006)
29. Spring, Summer, Fall, Winter… and Spring (Kim, 2003)
30. Morvern Callar (Ramsay, 2002)
31. Kings & Queen (Desplechin, 2004)
32. George Washington (Green, 2000)
33. The Man Without a Past (Kaurismäki, 2002)
34. Code Unknown (Haneke, 2000)
35. My Winnipeg (Maddin, 2007)
36. Children of Men (Cuarón, 2006)
37. What Time Is It There? (Tsai, 2001)
38. Full Frontal (Soderbergh, 2002)
39. You Can Count on Me (Lonergan, 2000)
40. Happy-Go-Lucky (Leigh, 2008)
41. 12:08 East of Bucharest (Porumboiu, 2006)
42. Million Dollar Baby (Eastwood, 2004)
43. The Piano Teacher (Haneke, 2001)
44. Three Times (Hou, 2005)
45. No Country for Old Men (Coen Brothers, 2007)
46. Y tu mamá también (Cuarón, 2001)
47. Eternal Sunshine of the Spotless Mind (Gondry, 2004)
48. The Little Matchgirl (Allers, 2006)
49. Saraband (Bergman, 2003)
50. Of Time and the City (Davies, 2008)
51. Brokeback Mountain (Lee, 2005)
52. Time Out (Cantet, 2001)
53. Irréversible (Noé, 2002)
54. Coraline (Selick, 2009)
55. There Will Be Blood (Anderson, 2007)
56. Ocean’s Twelve (Soderbergh, 2004)
57. The Wind That Shakes the Barley (Loach, 2006)
58. Finding Nemo (Stanton, 2003)
59. The Limits of Control (Jarmusch, 2009)
60. Vera Drake (Leigh, 2004)
61. Bloody Sunday (Greengrass, 2002)
62. Spirited Away (Miyazaki, 2001)
63. The Five Obstructions (von Trier and Leth, 2003)
64. A Christmas Tale (Desplechin, 2008)
65. demonlover (Assayas, 2002)
66. The Death of Mr. Lazarescu (Puiu, 2005)
67. Up (Docter, 2009)
68. The Gleaners and I (Varda, 2000)
69. The Assassination of Jesse James by the Coward Robert Ford (Dominik, 2007)
70. Kill Bill, Vol. 1/Kill Bill, Vol. 2 (Tarantino, 2003-’04)
71. The Day I Became a Woman (Meshkini, 2000)
72. Blissfully Yours (Weerasethakul, 2002)
73. Monsters, Inc. (Docter, 2001)
74. Songs from the Second Floor (Andersson, 2000)
75. Burn After Reading (Coen Brothers, 2008)
76. Gerry (Van Sant, 2002)
77. The Proposition (Hillcoat, 2005)
78. Russian Ark (Sokurov, 2002)
79. Che: Parts One & Two (Soderbergh, 2008)
80. Far from Heaven Haynes, 2002)
81. A Time for Drunken Horses (Ghobadi, 2000)
82. Broken Flowers (Jarmusch, 2005)
83. Oldboy (Park, 2003)
84. Amores perros (González Iñárritu, 2000)
85. Man Push Cart (Bahrani, 2005)
86. The Edge of Heaven (Akin, 2007)
87. The Three Burials of Melquiades Estrada (Jones, 2005)
88. The Story of Marie and Julien (Rivette, 2003)
89. La ciénaga (Martel, 2001)
90. Crouching Tiger, Hidden Dragon (Lee, 2000)
91. Summer Hours (Assayas, 2008)
92. War of the Worlds (Spielberg, 2005)
93. Birth (Glazer, 2004)
94. Bad Education (Almodóvar, 2004)
95. Away from Her (Polley, 2006)
96. Batman Begins (Nolan, 2005)
97. Zodiac (Fincher, 2007)
98. The Descent (Marshall, 2005)
99. Millennium Actress (Kon, 2001)
100. Old Joy (Reichardt, 2006)