I found over 18 lists of “Best Documentary Films of All Time” on the Internet and combined them into one meta-list.  Here are the results, organized chronologically. This list includes every documentary on at least three of the lists. I’ve included the number of lists that the film is on.  If I’ve seen the documentary, I’ve also included my 1-10 rating, For a version of this list organized by rank (i.e., with the films on the most lists at the top), go here.

The Early Years: 1922-1955
Nanook of the North (US, 1922) Dir: Robert J. Flaherty (8) (on 9 lists)
Man With a Movie Camera (USSR, 1929) Dir: Dziga Vertov (10) (on 11 lists)
Triumph of the Will (Germany, 1934) Dir: Leni Riefenstahl (8) (on 4 lists)
Night and Fog (Nuit et brouillard) (France, 1955) Dir: Alain Resnais (10) (on 9 lists)

The 1960s
Chronicle of a Summer (France, 1961) Dir: Jean Rouch (on 3 lists)
Seven-Up (UK, 1964) Dir: Paul Almond (on 12 lists)
The War Game (UK, 1965) Dir: Peter Watkins (8) (on 3 lists)
Dont Look Back (US, 1967) Dir: D.A. Pennebaker (8) (on 10 lists)
Titicut Follies (US, 1967) Dir: Frederick Wiseman (on 6 lists)
Salesman (US, 1968) Dir: Albert Maysles, David Maysles & Charlotte Zwerin (on 9 lists)
High School (US, 1968) Dir: Frederick Wiseman (on 3 lists)
Symbiopsychotaxiplasm: Take One (US, 1968) Dir: William Greaves (10) (on 3 lists)
In the Year of the Pig (US, 1968) Dir: Emile de Antonio (on 3 lists)
The Sorrow and the Pity (France, 1969) Dir: Marcel Ophüls (on 6 lists)

The 1970s
14-Up (UK, 1970) Dir: Michael Apted (on 12 lists)
Gimme Shelter (US, 1970) Dir: Albert Maysles, David Maysles & Charlotte Zwerin (9) (on 10 lists)
Woodstock (US, 1970) Dir: Michael Wadleigh (8) (on 6 lists)
F for Fake (France/Iran/West Germany, 1973) Dir: Orson Welles (on 8 lists)
Hearts and Minds (US, 1974) Dir: Peter Davis (on 4 lists)
Grey Gardens (UK, 1975) Dir: Albert Maysles, David Maysles, Ellen Hovde & Muffie Meyer (9) (on 12 lists)
Welfare (US, 1975) Dir: Frederick Wiseman (on 3 lists)
Harlan County, USA (US, 1976) Dir: Barbara Kopple (on 10 lists)
21-Up (UK, 1977) Dir: Michael Apted (on 12 lists)
The Last Waltz (US, 1978) Dir: Martin Scorsese (9) (on 9 lists)
The Battle of Chile (Chile, 1975, 1976, 1979) Dir: Patricio Guzman (on 7 lists)

The 1980s
Koyaanisqatsi (US, 1982) Dir: Godfrey Reggio (9) (on 9 lists)
Burden of Dreams (US, 1982) Dir: Les Blank (7) (on 4 lists)
Sans Soleil (France, 1983) Dir: Chris Marker (9) (on 7 lists)
28-Up (UK, 1984) Dir: Michael Apted (9) (on 12 lists)
The Times of Harvey Milk (US, 1984) Dir: Rob Epstein (9) (on 6 lists)
Stop Making Sense (US, 1984) Dir: Jonathan Demme (9) (on 5 lists)
Streetwise (US, 1984) Dir: Martin Bell (9) (on 3 lists)
Shoah (France, 1985) Dir: Claude Lanzmann (on 11 lists)
Sherman’s March (US, 1986) Dir: Ross McElwee (9) (on 7 lists)
The Thin Blue Line (US, 1988) Dir: Errol Morris (10) (on 18 lists)
Roger & Me (US, 1989) Dir: Michael Moore (8) (on 8 lists)

The 1990s
Paris is Burning (US, 1990) Dir: Jennie Livingston (8) (on 5 lists)
35-Up (UK, 1991) Dir: Michael Apted (8) (on 12 lists)
Hearts of Darkness: A Filmmaker’s Apocalypse (US, 1991) Dir: Fax Bahr, George Hickenlooper, Eleanor Coppola (9) (on 8 lists)
Brother’s Keeper (US, 1992) Dir: Joe Berlinger & Bruce Sinofsky (9) (on 3 lists)
Lessons of Darkness (Germany/France/UK, 1992) Dir: Werner Herzog (on 3 lists)
Hoop Dreams (US, 1994) Dir: Steve James (9) (on 15 lists)
Crumb (US, 1994) Dir: Terry Zwigoff (9) (on 11 lists)
When We Were Kings (US, 1996) Dir: Leon Gast (8) (on 9 lists)
Paradise Lost: The Child Murders at Robin Hood Hills (US, 1996) Dir: Joe Berlinger & Bruce Sinofsky (on 4 lists)
42-Up (UK, 1998) Dir: Michael Apted (8) (on 12 lists)
Buena Vista Social Club (Germany/US/UK/France/Cuba, 1998) Dir: Wim Wenders (8) (on 6 lists)
Little Dieter Needs to Fly (Germany/UK/France, 1998) Dir: Werner Herzog (9) (on 4 lists)
American Movie (US, 1999) Dir: Chris Smith (8) (on 4 lists)

The 2000s
The Gleaners & I (France, 2000) Dir: Agnès Varda (on 7 lists)
Dark Days (US, 2000) Dir: Marc Singer (on 5 lists)
Bowling for Columbine (US, 2002) Dir: Michael Moore (7) (on 12 lists)
Spellbound (US, 2002) Dir: Jeffrey Blitz (9) (on 10 lists)
Bus 174 (Brazil, 2002) Dir: José Padilha & Felipe Lacerda (8) (on 6 lists)
Winged Migration (France/Italy/Germany/Switzerland, 2002) Dir: Jacques Perrin, Jacques Cluzaud & Michel Debats (8) (on 3 lists)
The Fog of War: Eleven Lessons from the Life of Robert S. McNamara (US, 2003) Dir: Errol Morris (9) (on 14 lists)
Capturing the Friedmans (US, 2003) Dir: Andrew Jarecki (10) (on 9 lists)
Touching the Void (UK, 2003) Dir: Kevin Macdonald (9) (on 5 lists)
Tarnation (US, 2003) Dir: Jonathan Caouette (10) (on 4 lists)
To Be and to Have (Être et Avoir) (France, 2003) Dir: Nicolas Philibert (8) (on 3 lists)
Fahrenheit 9/11 (US, 2004) Dir: Michael Moore (10) (on 8 lists)
Super Size Me (US, 2004) Dir: Morgan Spurlock (8) (on 8 lists)
Born into Brothels: Calcutta’s Red Light Kids (US/India, 2004) Dir: Zana Briski & Ross Kauffman (10) (on 5 lists)
Metallica: Some Kind of Monster (US, 2004) Dir: Joe Berlinger & Bruce Sinofsky (on 5 lists)
Dig! (US, 2004) Dir: Ondi Timoner (on 3 lists)
Grizzly Man (US, 2005) Dir: Werner Herzog (10) (on 16 lists)
49-Up (UK, 2005) Dir: Michael Apted (8) (on 12 lists)
Murderball (US, 2005) Dir: Henry Alex Rubin & Dana Adam Shapiro (on 6 lists)
Enron: The Smartest Guys in the Room (US, 2005) Dir: Alex Gibney (on 6 lists)
March of the Penguins (France, 2005) Dir: Luc Jacquet (9) (on 5 lists)
Planet Earth (UK, 2006) Dir: Alastair Fothergill (9) (on 3 lists)
When the Levees Broke: A Requiem in Four Acts (US, 2006) Dir: Spike Lee (on 3 lists)
Deliver Us From Evil (US, 2006) Dir: Amy Berg (on 3 lists)
An Inconvenient Truth (US, 2006) Dir: Davis Guggenheim (on 8 lists)
Taxi to the Dark Side (US, 2007) Dir: Alex Gibney (on 7 lists)
The King of Kong: A Fistful of Quarters (US, 2007) Dir: Seth Gordon (on 5 lists)
Helvetica (US, 2007) Dir: Gary Hustwit (on 3 lists)
Anvil! The Story of Anvil (US, 2007) Dir: Sacha Gervasi (on 3 lists)
Man on Wire (UK, 2008) Dir: James Marsh (8) (on 16 lists)
Waltz with Bashir (Israel, 2008) Dir: Ari Folman (on 9 lists)
Food, Inc. (US, 2008) Dir: Robert Kenner (9) (on 5 lists)
Dear Zachary: A Letter to a Son about His Father (US, 2008) Dir: Kurt Kuenne (on 3 lists)
Last Train Home (Canada, 2009) Dir: Lixin Fan (on 4 lists)

The 2010s
Exit Through the Gift Shop (UK, 2010) Dir: Banksy (7) (on 10 lists)
Inside Job (US, 2010) Dir: Charles Ferguson (9) (on 8 lists)
Marwencol (US, 2010) Dir: Jeff Malmberg (9) (on 7 lists)
Cave of Forgotten Dreams (Canada/US/France/Germany/UK, 2010) Dir: Werner Herzog (10) (on 7 lists)
Bill Cunningham New York (US, 2010) Dir: Richard Press (7) (on 5 lists)
Nostalgia for the Light (France/Chile/Germany/Spain/US, 2010) Dir: Patricio Guzmán (on 5 lists)
Catfish (US, 2010) Dir: Henry Joost & Ariel Schulman (7) (on 4 lists)
Senna (UK/France, 2010) Dir: Asif Kapadia (on 4 lists)
Gasland (US, 2010) Dir: Josh Fox (on 3 lists)
Jiro Dreams of Sushi (US, 2011) Dir: David Gelb (on 6 lists)
The Interrupters (US, 2011) Dir: Steve James (on 3 lists)
56-Up (UK, 2012) Dir: Michael Apted (on 12 lists)
How to Survive a Plague (US, 2012) Dir: David France (7) (on 5 lists)
This Is Not a Film (Iran, 2012) Dir: Jafar Panahi & Mojtaba Mirtahmasb (on 5 lists)
The Act of Killing (Norway/Denmark/UK, 2012) Dir: Joshua Oppenheimer (10) (on 4 lists)
Stories We Tell (Canada, 2012) Dir: Sarah Polley (on 3 lists)
Blackfish (US, 2013) Dir: Gabriela Cowperthwaite (7) (on 4 lists)
Citizenfour (US/Germany, 2014) Dir: Laura Poitras (on 3 lists)
The Overnighters (US, 2014) Dir: Jesse Moss (on 3 lists)
The Look of Silence (Denmark/Finland/France/Germany, et al., 2015) Dir: Joshua Oppenheimer (on 5 lists)
Amy (UK, 2015) Dir: Asif Kapadia (8) (on 4 lists)
O.J.: Made in America (US, 2016) Dir: Ezra Edelman (10) (on 3 lists)
I Am Not Your Negro (France/US/Belgium/Switzerland, 2016) Dir: Raoul Peck (on 3 lists)