I’ve seen 47 of these. The bolds I believe belong on this list. I generally liked all the rest of these films except for The Tree of Life and A Serious Man. Melancholia would have been included as one I didn't like if I had the stomach to finish it. In the Mood for Love, Boyhood, A Separation and No Country for Old Men are in my overrated films lists but I still felt they were good films.
100. Requiem for a Dream (Darren Aronofsky, 2000)
96. Finding Nemo (Andrew Stanton, 2003)
94. Let the Right One In (Tomas Alfredson, 2008)
93. Ratatouille (Brad Bird, 2007)
90. The Pianist (Roman Polanski, 2002)
87. Amélie (Jean-Pierre Jeunet, 2001)
86. Far From Heaven (Todd Haynes, 2002)
84. Her (Spike Jonze, 2013)
83. A.I. Artificial Intelligence (Steven Spielberg, 2001)
82. A Serious Man (Joel and Ethan Coen, 2009)
79. Almost Famous (Cameron Crowe, 2000)
78. The Wolf of Wall Street (Martin Scorsese, 2013)
77. The Diving Bell and the Butterfly (Julian Schnabel, 2007)
73. Before Sunset (Richard Linklater, 2004)
68. The Royal Tenenbaums (Wes Anderson, 2001)
67. The Hurt Locker (Kathryn Bigelow, 2008)
66. Spring, Summer, Fall, Winter…and Spring (Kim Ki-duk, 2003)
62. Inglourious Basterds (Quentin Tarantino, 2009)
59. A History of Violence (David Cronenberg, 2005)
57. Zero Dark Thirty (Kathryn Bigelow, 2012)
53. Moulin Rouge! (Baz Luhrmann, 2001)
51. Inception (Christopher Nolan, 2010)
44. 12 Years a Slave (Steve McQueen, 2013)
40. Brokeback Mountain (Ang Lee, 2005)
38. City of God (Fernando Meirelles and Kátia Lund, 2002)
35. Crouching Tiger, Hidden Dragon (Ang Lee, 2000)
33. The Dark Knight (Christopher Nolan, 2008)
32. The Lives of Others (Florian Henckel von Donnersmarck, 2006)
30. Oldboy (Park Chan-wook, 2003)
29. WALL-E (Andrew Stanton, 2008)
27. The Social Network (David Fincher, 2010)
25. Memento (Christopher Nolan, 2000)
22. Lost in Translation (Sofia Coppola, 2003)
21. The Grand Budapest Hotel (Wes Anderson, 2014)
19. Mad Max: Fury Road (George Miller, 2015)
17. Pan's Labyrinth (Guillermo Del Toro, 2006)
13. Children of Men (Alfonso Cuarón, 2006)
12. Zodiac (David Fincher, 2007)
10. No Country for Old Men (Joel and Ethan Coen, 2007)
9. A Separation (Asghar Farhadi, 2011)
7. The Tree of Life (Terrence Malick, 2011)
6. Eternal Sunshine of the Spotless Mind (Michel Gondry, 2004)
5. Boyhood (Richard Linklater, 2014)
4. Spirited Away (Hayao Miyazaki, 2001)
3. There Will Be Blood (Paul Thomas Anderson, 2007)
2. In the Mood for Love (Wong Kar-wai, 2000)
1. Mulholland Drive (David Lynch, 2001)