…here is a great list of 100 best documentary films by filmspotting.net
100. My Best Fiend: Klaus Kinski (Werner Herzog, 1999)
99. Trekkies (Roger Nygard, 1997)
98. Bus 174 (José Padilha, 2002)
97. La Danse: The Paris Opera Ballet (Frederick Wiseman, 2009)
96. Control Room (Jehane Noujaim, 2004)
95. Fahrenheit 9/11 (Michael Moore, 2004)
94. 24 City (Jia Zhangke, 2008)
93. Stranded: I’ve Come from a Plane That Crashed on the Mountains (Gonzalo Arijon, 2007)
92. For All Mankind (Al Reinert, 1989)
91. Dear Zachary: A Letter to a Son About His Father (Kurt Kuenne, 2008)
90. The Elephant Will Never Forget (John Krish, 1953)
89. An Inconvenient Truth (Davis Guggenheim, 2006)
88. The House Is Black (Forugh Farrokhzad, 1963)
87. Catfish (Henry Joost & Ariel Schulman, 2010)
86. Enron: The Smartest Guys in the Room (Alex Gibney, 2005)
85. Ryan (Chris Landreth, 2004)
84. Dogtown and Z-Boys (Stacy Peralta, 2001)
83. Restrepo (Tim Hetherington & Sebastian Junger, 2010)
82. Koyaanisqatsi (Godfrey Reggio, 1982)
81. Murder on a Sunday Morning (Jean-Xavier de Lestrade, 2001)
80. Street Fight (Marshall Curry, 2005)
79. When the Levees Broke: A Requiem in Four Acts (Spike Lee, 2006)
78. One Day in September (Kevin Macdonald, 1999)
77. Jesus Camp (Heidi Ewing & Rachel Grady, 2006)
76. Standard Operating Procedure (Errol Morris, 2008)
75. The Five Obstructions (Jørgen Leth & Lars von Trier, 2003)
74. The Last Waltz (Martin Scorsese, 1978)
73. Winged Migration (Jacques Perrin, 2001)
72. Gates of Heaven (Errol Morris, 1978)
71. Encounters at the End of the World (Werner Herzog, 2007)
70. Man of Aran (Robert Flaherty, 1934)
69. The Power of Nightmares: The Rise of the Politics of Fear (Adam Curtis, 2004)
68. The Devil and Daniel Johnston (Jeff Feuerzeig, 2005)
67. Hearts and Minds (Peter Davis, 1974)
66. Super Size Me (Morgan Spurlock, 2004)
65. A Time for Burning (Barbara Connell & Bill Jersey, 1967)
64. Shoah (Claude Lanzmann, 1985)
63. This Film Is Not Yet Rated (Kirby Dick, 2006)
62. The Kid Stays in the Picture (Nanette Burstein & Brett Morgen, 2002)
61. Blood of the Beasts (Georges Franju, 1949)
60. Young@Heart (Stephen Walker, 2007)
59. In the Shadow of the Moon (David Sington, 2007)
58. Stevie (Steve James, 2002)
57. Anvil! The Story of Anvil (Sacha Gervasi, 2008)
56. Lost in La Mancha (Keith Fulton & Louis Pepe, 2002)
55. The Cove (Louie Psihoyos, 2009)
54. Baseball (Ken Burns, 1994)
53. My Kid Could Paint That (Amir Bar-Lev, 2007)
52. Baraka (Ron Fricke, 1992)
51. Sicko (Michael Moore, 2007)
50. Inside Job (Charles Ferguson, 2010)
49. Paradise Lost: The Child Murders at Robin Hood Hills (Joe Berlinger & Bruce Sinofsky, 1996)
48. Up the Yangtze (Yung Chang, 2007)
47. Crumb (Terry Zwigoff, 1994)
46. Capturing the Friedmans (Andrew Jarecki, 2003)
45. The Beaches of Agnès (Agnès Varda, 2008)
44. Spellbound (Jeffrey Blitz, 2002)
43. American Movie (Chris Smith, 1999)
42. Dark Days (Marc Singer, 2000)
41. High School (Frederick Wiseman, 1968)
40. Nanook of the North (Robert Flaherty, 1922)
39. Little Dieter Needs to Fly (Werner Herzog, 1998)
38. Murderball (Henry Alex Rubin & Dana Adam Shapiro, 2005)
37. When We Were Kings (Leon Gast, 1996)
36. Sans soleil (Chris Marker, 1983)
35. The Gleaners & I (Agnès Varda, 2000)
34. Streetwise (Martin Bell, 1984)
33. Wordplay (Patrick Creadon, 2006)
32. Lake of Fire (Tony Kaye, 2006)
31. Woodstock (Michael Wadleigh, 1970)
30. Salesman (Albert Maysles, David Maysles & Charlotte Zwerin, 1968)
29. Los Angeles Plays Itself (Thom Andersen, 2003)
28. No Direction Home: Bob Dylan (Martin Scorsese, 2005)
27. Grey Gardens (David Maysles, Albert Maysles, Ellen Hovde & Muffie Meyer, 1975)
26. Gimme Shelter (Albert Maysles, David Maysles & Charlotte Zwerin, 1970)
25. The Civil War (Ken Burns, 1990)
24. My Winnipeg (Guy Maddin, 2007)
23. F for Fake (Orson Welles, 1973)
22. Waltz with Bashir (Ari Folman, 2008)
21. Roger & Me (Michael Moore, 1989)
20. Titicut Follies (Frederick Wiseman, 1967)
19. Man on Wire (James Marsh, 2008)
18. Burden of Dreams (Les Blank, 1982)
17. The Up Series (Paul Almond & Michael Apted, 1964-2005)
16. Bowling for Columbine (Michael Moore, 2002)
15. Hearts of Darkness: A Filmmaker’s Apocalypse (Fax Bahr & George Hickenlooper, 1991)
14. The King of Kong: A Fistful of Quarters (Seth Gordon, 2007)
13. The Fog of War: Eleven Lessons from the Life of Robert S. McNamara (Errol Morris, 2003)
12. Dont Look Back (D.A. Pennebaker, 1967)
11. Harlan County U.S.A. (Barbara Kopple, 1976)
10. Touching the Void (Kevin Macdonald, 2003)
9. Man with a Movie Camera (Dziga Vertov, 1929)
8. Planet Earth (Alastair Fothergill, 2006)
7. Exit Through the Gift Shop (Banksy, 2010)
6. The Times of Harvey Milk (Rob Epstein, 1984)
5. Grizzly Man (Werner Herzog, 2005)
4. The Thin Blue Line (Errol Morris, 1988)
3. Stop Making Sense (Jonathan Demme, 1984)
2. Hoop Dreams (Steve James, 1994)
1. Night and Fog (Alain Resnais, 1955)