I found over 18 lists of “Best Documentary Films of All Time” on the Internet and combined them into one list.  Here are the results, organized by rank (i.e., with the films on the most lists at the top). This list includes every documentary on at three or more of the original source lists. I have not seen all these films, but for those I’ve seen, I’ve included my 1-10 rating. For a version of this list organized chronologically, go here.

On 18 lists
The Thin Blue Line (US, 1988) Dir: Errol Morris (10)

On 16 lists
Grizzly Man (US, 2005) Dir: Werner Herzog (10)
Man on Wire (UK, 2008) Dir: James Marsh (8)

On 15 lists
Hoop Dreams (US, 1994) Dir: Steve James (9)

On 14 lists
The Fog of War: Eleven Lessons from the Life of Robert S. McNamara (US, 2003) Dir: Errol Morris (9)

On 12 lists
The Up Series (UK, 1964- )
     Seven-Up (UK, 1964) Dir: Paul Almond
     14-Up (UK, 1970) Dir: Michael Apted
     21-Up (UK, 1977) Dir: Michael Apted
     28-Up (UK, 1984) Dir: Michael Apted (9)
     35-Up (UK, 1991) Dir: Michael Apted (8)
     42-Up (UK, 1998) Dir: Michael Apted (8)
     49-Up (UK, 2005) Dir: Michael Apted (8)
     56-Up (UK, 2012) Dir: Michael Apted
Grey Gardens (UK, 1975) Dir: Albert Maysles, David Maysles, Ellen Hovde & Muffie Meyer (9)
Bowling for Columbine (US, 2002) Dir: Michael Moore (7)

On 11 lists
Man With a Movie Camera (USSR, 1929) Dir: Dziga Vertov (10)
Shoah (France, 1985) Dir: Claude Lanzmann
Crumb (US, 1994) Dir: Terry Zwigoff (9)

On 10 lists
Dont Look Back (US, 1967) Dir: D.A. Pennebaker (8)
Gimme Shelter (US, 1970) Dir: Albert Maysles, David Maysles & Charlotte Zwerin (9)
Harlan County, USA (US, 1976) Dir: Barbara Kopple
Spellbound (US, 2002) Dir: Jeffrey Blitz (9)
Exit Through the Gift Shop (UK, 2010) Dir: Banksy (7)

On 9 lists
Nanook of the North (US, 1922) Dir: Robert J. Flaherty (8)
Night and Fog (Nuit et brouillard) (France, 1955) Dir: Alain Resnais (10)
Salesman (US, 1968) Dir: Albert Maysles, David Maysles & Charlotte Zwerin
The Last Waltz (US, 1978) Dir: Martin Scorsese (9)
Koyaanisqatsi (US, 1982) Dir: Godfrey Reggio (9)
When We Were Kings (US, 1996) Dir: Leon Gast (8)
Capturing the Friedmans (US, 2003) Dir: Andrew Jarecki (10)
Waltz with Bashir (Israel, 2008) Dir: Ari Folman

On 8 lists
F for Fake (France/Iran/West Germany, 1973) Dir: Orson Welles
Roger & Me (US, 1989) Dir: Michael Moore (8)
Hearts of Darkness: A Filmmaker’s Apocalypse (US, 1991) Dir: Fax Bahr, George Hickenlooper, Eleanor Coppola (9)
Fahrenheit 9/11 (US, 2004) Dir: Michael Moore (10)
Super Size Me (US, 2004) Dir: Morgan Spurlock (8)
An Inconvenient Truth (US, 2006) Dir: Davis Guggenheim
Inside Job (US, 2010) Dir: Charles Ferguson (9)

On 7 lists
The Battle of Chile (Chile, 1975, 1976, 1979) Dir: Patricio Guzman
Sans Soleil (France, 1983) Dir: Chris Marker (9)
Sherman’s March (US, 1986) Dir: Ross McElwee (9)
The Gleaners & I (France, 2000) Dir: Agnès Varda
Taxi to the Dark Side (US, 2007) Dir: Alex Gibney
Marwencol (US, 2010) Dir: Jeff Malmberg (9)
Cave of Forgotten Dreams (Canada/US/France/Germany/UK, 2010) Dir: Werner Herzog (10)

On 6 lists
Titicut Follies (US, 1967) Dir: Frederick Wiseman
The Sorrow and the Pity (France, 1969) Dir: Marcel Ophüls
Woodstock (US, 1970) Dir: Michael Wadleigh (8)
The Times of Harvey Milk (US, 1984) Dir: Rob Epstein (9)
Buena Vista Social Club (Germany/US/UK/France/Cuba, 1998) Dir: Wim Wenders (8)
Bus 174 (Brazil, 2002) Dir: José Padilha & Felipe Lacerda (8)
Murderball (US, 2005) Dir: Henry Alex Rubin & Dana Adam Shapiro
Enron: The Smartest Guys in the Room (US, 2005) Dir: Alex Gibney
Jiro Dreams of Sushi (US, 2011) Dir: David Gelb

On 5 lists
Stop Making Sense (US, 1984) Dir: Jonathan Demme (9)
Paris is Burning (US, 1990) Dir: Jennie Livingston (8)
Dark Days (US, 2000) Dir: Marc Singer
Touching the Void (UK, 2003) Dir: Kevin Macdonald (9)
Born into Brothels: Calcutta’s Red Light Kids (US/India, 2004) Dir: Zana Briski & Ross Kauffman (10)
Metallica: Some Kind of Monster (US, 2004) Dir: Joe Berlinger & Bruce Sinofsky
March of the Penguins (France, 2005) Dir: Luc Jacquet (9)
The King of Kong: A Fistful of Quarters (US, 2007) Dir: Seth Gordon
Food, Inc. (US, 2008) Dir: Robert Kenner (9)
Bill Cunningham New York (US, 2010) Dir: Richard Press (7)
Nostalgia for the Light (France/Chile/Germany/Spain/US, 2010) Dir: Patricio Guzmán
How to Survive a Plague (US, 2012) Dir: David France (7)
This Is Not a Film (Iran, 2012) Dir: Jafar Panahi & Mojtaba Mirtahmasb
The Look of Silence (Denmark/Finland/France/Germany, et al., 2015) Dir: Joshua Oppenheimer

On 4 lists
Triumph of the Will (Germany, 1934) Dir: Leni Riefenstahl (8)
Hearts and Minds (US, 1974) Dir: Peter Davis
Burden of Dreams (US, 1982) Dir: Les Blank (7)
Paradise Lost: The Child Murders at Robin Hood Hills (US, 1996) Dir: Joe Berlinger & Bruce Sinofsky
Little Dieter Needs to Fly (Germany/UK/France, 1998) Dir: Werner Herzog (9)
American Movie (US, 1999) Dir: Chris Smith (8)
Tarnation (US, 2003) Dir: Jonathan Caouette (10)
Last Train Home (Canada, 2009) Dir: Lixin Fan
Catfish (US, 2010) Dir: Henry Joost & Ariel Schulman (7)
Senna (UK/France, 2010) Dir: Asif Kapadia
The Act of Killing (Norway/Denmark/UK, 2012) Dir: Joshua Oppenheimer (10)
Blackfish (US, 2013) Dir: Gabriela Cowperthwaite (7)
Amy (UK, 2015) Dir: Asif Kapadia (8)

On 3 lists
Chronicle of a Summer (France, 1961) Dir: Jean Rouch
The War Game (UK, 1965) Dir: Peter Watkins (8)
High School (US, 1968) Dir: Frederick Wiseman
Symbiopsychotaxiplasm: Take One (US, 1968) Dir: William Greaves (10)
In the Year of the Pig (US, 1968) Dir: Emile de Antonio
Welfare (US, 1975) Dir: Frederick Wiseman
Streetwise (US, 1984) Dir: Martin Bell (9)
Brother’s Keeper (US, 1992) Dir: Joe Berlinger & Bruce Sinofsky (9)
Lessons of Darkness (Germany/France/UK, 1992) Dir: Werner Herzog
Winged Migration (France/Italy/Germany/Switzerland, 2002) Dir: Jacques Perrin, Jacques Cluzaud & Michel Debats (8)
To Be and to Have (Être et Avoir) (France, 2003) Dir: Nicolas Philibert (8)
Dig! (US, 2004) Dir: Ondi Timoner
Planet Earth (UK, 2006) Dir: Alastair Fothergill (9)
When the Levees Broke: A Requiem in Four Acts (US, 2006) Dir: Spike Lee
Deliver Us From Evil (US, 2006) Dir: Amy Berg
Helvetica (US, 2007) Dir: Gary Hustwit
Anvil! The Story of Anvil (US, 2007) Dir: Sacha Gervasi
Dear Zachary: A Letter to a Son about His Father (US, 2008) Dir: Kurt Kuenne
Gasland (US, 2010) Dir: Josh Fox
The Interrupters (US, 2011) Dir: Steve James
Stories We Tell (Canada, 2012) Dir: Sarah Polley
Citizenfour (US/Germany, 2014) Dir: Laura Poitras
The Overnighters (US, 2014) Dir: Jesse Moss
I Am Not Your Negro (France/US/Belgium/Switzerland, 2016) Dir: Raoul Peck
O.J.: Made in America (US, 2016) Dir: Ezra Edelman (10)