Let's get to the good part...

Best of 2000 - 2004

Here's the rest. The earlier genre-specific categories included 2005. This was mainly to include Batman Begins on the Action/Sci-Fi list. This main list does not include any movies from 2005. If it did The Interpreter might make it and Sin City definitely would. I tried to rank them in an order that would reflect their quality, but that's really hard to do. Mainly these are the best made movies that I enjoyed the most in a semi-rigid ranking. There is one made-for-HBO movie on the list (Angels in America). It was just too good to leave off the list.

50. Bamboozled (2000)
49. Confessions of a Dangerous Mind (2002)
48. Hotel Rwanda (2004)
47. Waking Life (2001)
46. Kinsey (2004)
45. Angels in America (2004)
44. Best in Show (2000)
43. Kill Bill: Vol. 1 (2003) / Kill Bill: Vol. 2 (2004)
42. Holes (2003)
41. Startup.com (2001)
40. Punch Drunk Love (2002)
39. Open Range (2003)
38. 25th Hour (2002)
37. Hedwig and the Angry Inch (2001)
36. Amelie (2001)
35. Shadow of the Vampire (2000)
34. Shattered Glass (2003)
33. Monsters Inc. (2001)
32. Sideways (2004)
31. Before Sunset (2004)
30. The Man Who Wasn’t There (2001)
29. The Cooler (2003)
28. The Lord of the Rings: The Return of the King (2003)
27. O Brother, Where Art Thou? (2000)
26. Almost Famous (2000)
25. You Can Count on Me (2000)
24. Harry Potter & the Chamber of Secrets (2002) / Harry Potter & the Prisoner of Azkaban (2004)
23. Ghost World (2001)
22. Sexy Beast (2001)
21. Chicago (2002)
20. Capturing the Friedmans (2003)
19. Mulholland Dr. (2001)
18. Crouching Tiger, Hidden Dragon (2000)
17. Memento (2001)
16. Traffic (2000)
15. Mean Creek (2004)
14. Jesus’ Son (2000)
13. Black Hawk Down (2001)
12. The Lord of the Rings: The Fellowship of the Rings (2001)
11. Spirited Away (2002)
10. The Royal Tenenbaums (2001)
9. Y tu mama tambien (2001)
8. American Splendor (2003)
7. In the Bedroom (2001)
6. Wonder Boys (2000)
5. Adaptation (2002)
4. Eternal Sunshine of the Spotless Mind (2004)
3. Lost in Translation (2003)
2. Requiem for a Dream (2000)
1. City of God (2002)