I found over 25 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 or nonfiction film 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 24 lists
The Thin Blue Line (US, 1988) Dir: Errol Morris (10)

On 23 lists
Grizzly Man (US, 2005) Dir: Werner Herzog (10)

Man on Wire (UK, 2008) Dir: James Marsh (8)

On 21 lists
Hoop Dreams (US, 1994) Dir: Steve James (9)
On 20 lists
Grey Gardens (UK, 1975) Dir: Albert Maysles, David Maysles, Ellen Hovde & Muffie Meyer (9)

On 18 lists
Shoah (France, 1985) Dir: Claude Lanzmann

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

On 17 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
63-Up (UK, 2019) Dir: Michael Apted

Bowling for Columbine (US, 2002) Dir: Michael Moore (7)

On 16 lists
Man With a Movie Camera (USSR, 1929) Dir: Dziga Vertov (10)

Gimme Shelter (US, 1970) Dir: Albert Maysles, David Maysles & Charlotte Zwerin (9)

Harlan County, USA (US, 1976) Dir: Barbara Kopple

Crumb (US, 1994) Dir: Terry Zwigoff (9)

On 15 lists
Dont Look Back (US, 1967) Dir: D.A. Pennebaker (8)

Koyaanisqatsi (US, 1982) Dir: Godfrey Reggio (9)

Waltz with Bashir (Israel, 2008) Dir: Ari Folman (9)

Exit Through the Gift Shop (UK, 2010) Dir: Banksy (7)

On 14 lists
Night and Fog (Nuit et brouillard) (France, 1955) Dir: Alain Resnais (10)

F for Fake (France/Iran/West Germany, 1973) Dir: Orson Welles

The Last Waltz (US, 1978) Dir: Martin Scorsese (9)

Hearts of Darkness: A Filmmaker’s Apocalypse (US, 1991) Dir: Fax Bahr, George Hickenlooper, Eleanor Coppola (9)

On 13 lists
Nanook of the North (US, 1922) Dir: Robert J. Flaherty (8)

Salesman (US, 1968) Dir: Albert Maysles, David Maysles & Charlotte Zwerin

The Times of Harvey Milk (US, 1984) Dir: Rob Epstein (9)

When We Were Kings (US, 1996) Dir: Leon Gast (8)

Spellbound (US, 2002) Dir: Jeffrey Blitz (9)

Capturing the Friedmans (US, 2003) Dir: Andrew Jarecki (10)

On 12 lists
Sans Soleil (France, 1983) Dir: Chris Marker (9)

Paris is Burning (US, 1990) Dir: Jennie Livingston (8)

The Gleaners & I (France, 2000) Dir: Agnès Varda

On 11 lists
Woodstock (US, 1970) Dir: Michael Wadleigh (8)

The Battle of Chile (Chile, 1975, 1976, 1979) Dir: Patricio Guzman
Fahrenheit 9/11 (US, 2004) Dir: Michael Moore (10)

An Inconvenient Truth (US, 2006) Dir: Davis Guggenheim

Inside Job (US, 2010) Dir: Charles Ferguson (9)

Amy (UK, 2015) Dir: Asif Kapadia (8)

On 10 lists
Titicut Follies (US, 1967) Dir: Frederick Wiseman

Stop Making Sense (US, 1984) Dir: Jonathan Demme (9)

Roger & Me (US, 1989) Dir: Michael Moore (8)

Super Size Me (US, 2004) Dir: Morgan Spurlock (8)

Jiro Dreams of Sushi (US, 2011) Dir: David Gelb
The Act of Killing (Norway/Denmark/UK, 2012) Dir: Joshua Oppenheimer (10)

The Look of Silence (Denmark/Finland/France/Germany, et al., 2015) Dir: Joshua Oppenheimer

On 9 lists
The Sorrow and the Pity (France, 1969) Dir: Marcel Ophüls

Burden of Dreams (US, 1982) Dir: Les Blank (7)

Sherman’s March (US, 1986) Dir: Ross McElwee (9)

Buena Vista Social Club (Germany/US/UK/France/Cuba, 1998) Dir: (8)

American Movie (US, 1999) Dir: Chris Smith (8)

The King of Kong: A Fistful of Quarters (US, 2007) Dir: Seth Gordon

Cave of Forgotten Dreams (Canada/US/France/Germany/UK, 2010) Dir: Werner Herzog (10)
On 8 lists
Hearts and Minds (US, 1974) Dir: Peter Davis

Metallica: Some Kind of Monster (US, 2004) Dir: Joe Berlinger & Bruce Sinofsky

Murderball (US, 2005) Dir: Henry Alex Rubin & Dana Adam Shapiro

Enron: The Smartest Guys in the Room (US, 2005) Dir: Alex Gibney

Taxi to the Dark Side (US, 2007) Dir: Alex Gibney

Marwencol (US, 2010) Dir: Jeff Malmberg (9)

How to Survive a Plague (US, 2012) Dir: David France (7)

I Am Not Your Negro (France/US/Belgium/Switzerland, 2016) Dir: Raoul Peck (8)

O.J.: Made in America (US, 2016) (TV series) Dir: Ezra Edelman (10)

On 7 lists
Paradise Lost: The Child Murders at Robin Hood Hills (US, 1996) Dir: Joe Berlinger & Bruce Sinofsky

Dark Days (US, 2000) Dir: Marc Singer

Bus 174 (Brazil, 2002) Dir: José Padilha & Felipe Lacerda (8)

Born into Brothels: Calcutta’s Red Light Kids (US/India, 2004) Dir: Zana Briski & Ross Kauffman (10)

Dear Zachary: A Letter to a Son about His Father (US, 2008) Dir: Kurt Kuenne

Senna (UK/France, 2010) Dir: Asif Kapadia

Nostalgia for the Light (France/Chile/Germany/Spain/US, 2010) Dir: Patricio Guzmán

This Is Not a Film (Iran, 2012) Dir: Jafar Panahi & Mojtaba Mirtahmasb (7)

Stories We Tell (Canada, 2012) Dir: Sarah Polley

Blackfish (US, 2013) Dir: Gabriela Cowperthwaite (7)

Citizenfour (US/Germany, 2014) Dir: Laura Poitras

On 6 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)

Welfare (US, 1975) Dir: Frederick Wiseman

Lessons of Darkness (Germany/France/UK, 1992) Dir: Werner Herzog

Touching the Void (UK, 2003) Dir: Kevin Macdonald (9)

Tarnation (US, 2003) Dir: Jonathan Caouette (10)

March of the Penguins (France, 2005) Dir: Luc Jacquet (9)

Food, Inc. (US, 2008) Dir: Robert Kenner (9)

Bill Cunningham New York (US, 2010) Dir: Richard Press (7)

Searching For Sugar Man (Sweden/UK/Finland 2012) Dir: Malik Bendjelloul

13th (US, 2016) Dir: Ava DuVernay (8)

On 5 lists
Triumph of the Will (Germany, 1935) Dir: Leni Riefenstahl (8)

Monterey Pop (US, 1968) Dir: D.A. Pennebaker (8)

In the Year of the Pig (US, 1968) Dir: Emile de Antonio

A Grin Without a Cat (France, 1977) Dir: Chris Marker

Histoire(s) du cinéma (France/Switzerland, 1998) Dir: Jean-Luc Godard

Little Dieter Needs to Fly (Germany/UK/France, 1998) Dir: Werner Herzog (9)

Dig! (US, 2004) Dir: Ondi Timoner

When the Levees Broke: A Requiem in Four Acts (US, 2006) Dir: Spike Lee

Kedi (Turkey, 2016) Dir: Ceyda Torun

Summer of Soul (…Or, When the Revolution Could Not Be Televised) (2021) Dir: Questlove

On 4 lists
Gates of Heaven (US, 1978) Dir: Errol Morris

Style Wars (US, 1983) Dir: Tony Silver

Streetwise (US, 1984) Dir: Martin Bell (9)

Close-Up (Iran, 1990) Dir: Abbas Kiarostami (10) 
D’Est (From the East) (Belgium/France/Portugal, 1993) Dir: Chantal Akerman

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)

Los Angeles Plays Itself (US, 2003) Dir: Thom Andersen (9)

The Devil and Daniel Johnston (US, 2005) Dir: Jeff Feuerzeig

Helvetica (US, 2007) Dir: Gary Hustwit

Anvil! The Story of Anvil (US, 2007) Dir: Sacha Gervasi

Sicko (US, 2007) Dir: Michael Moore (8)

The Beaches of Agnès (France, 2008) Dir: Agnès Varda

Last Train Home (Canada, 2009) Dir: Lixin Fan

Catfish (US, 2010) Dir: Henry Joost & Ariel Schulman (7)

Restrepo (US, 2010) Dir: Tim Hetherington & Sebastian Junger (8)

Project Nim (UK/US 2011) Dir: James Marsh

Pina (Germany, 2011) Dir: Wim Wenders (8)

West of Memphis (New Zealand/US, 2012) Dir: Amy Berg

The Queen of Versailles (US, 2012) Dir: Lauren Greenfield

Twenty Feet from Stardom (US, 2013) Dir: Morgan Neville (7)

The Overnighters (US, 2014) Dir: Jesse Moss

Life Itself (US, 2014) Dir: Steve James (7)

Weiner (US, 2016) Dir: Josh Kriegman & Elyse Steinberg (8)

Cameraperson (US, 2016) Dir: Kirsten Johnson

Free Solo (US, 2018) Elizabeth Chai Vasarhelyi & Jimmy Chin (8)

For Sama (Syria/UK/US 2019) Waad Al-Kateab & Edward Watts

All the Beauty and the Bloodshed (US, 2022) Laura Poitras (9)

On 3 lists
Arrival of a Train at La Ciotat (France, 1896) Dir: Auguste Lumière & Louis Lumière (6)

Land Without Bread (Spain, 1933) Dir: Luis Buñuel

Primary (US, 1960) Dir: Robert Drew

Tokyo Olympiad (Japan, 1965) Dir: Kon Ichikawa

Portrait of Jason (US, 1967) Dir: Shirley Clarke

The Hour of the Furnaces (Argentina, 1968) Dir: Octavio Getino & Fernando Solanas

Original Cast Album: Company (US, 1970) Dir: D. A. Pennebaker

Handsworth Songs (UK, 1986) Dir: John Akomfrah

The Emperor’s Naked Army Marches On (Japan, 1987) Dir: Kazuo Hara

For All Mankind (US, 1989) Dir: Al Reinert

Brother’s Keeper (US, 1992) Dir: Joe Berlinger & Bruce Sinofsky (9)

Baraka (US, 1992) Dir: Ron Fricke

The War Room (US, 1993) Dir: Chris Hegedus & D.A. Pennebaker (8)

Microcosmos (France/Switzerland/Italy/UK, 1996) Dir: Claude Nuridsany & Marie Pérennou (10)

The Kid Stays in the Picture (US, 2002) Dir: Nanette Burstein & Brett Morgen (8)

The Corporation (US, 2003) Dir: Jennifer Abbott & Mark Achbar (8)

The Wild Parrots of Telegraph Hill (US, 2003) Dir: Judy Irving (6)

Rivers and Tides (Germany/Finland/UK, 2003) Dir: Thomas Riedelsheimer

Tie Xi Qu: West of the Tracks (China, 2003) Dir: Wang Bing

Planet Earth (UK, 2006) (TV series) Dir: Alastair Fothergill (9)

Deliver Us From Evil (US, 2006) Dir: Amy Berg

This Film Is Not Yet Rated (US, 2006) Dir: Kirby Dick (7)

Jesus Camp (US, 2006) Dir: Heidi Ewing & Rachel Grady (8)

Encounters at the End of the World (US, 2007) Dir: Werner Herzog (9)

The Cove (US, 2009) Dir: Louie Psihoyos

The September Issue (US, 2009) Dir: R.J. Cutler

Gasland (US, 2010) Dir: Josh Fox

The Interrupters (US, 2011) Dir: Steve James

Room 237 (US, 2012) Dir: Rodney Ascher

Leviathan (US, 2012) Dir: Véréna Paravel & Lucien Castaing-Taylor

The Imposter (UK/US, 2012) Dir: Burt Layton

The Square (Egypt/US, 2013) Dir: Jehane Noujaim

Actress (US, 2014) Dir: Robert Greene

Going Clear: Scientology and the Prison of Belief (US, 2015) Dir: Alex Gibney (8)

Jane (US, 2017) Dir: Brett Morgen

Faces Places (France, 2017) Dir: Agnès Varda & JR (8)

Shirkers (Singapore/US/UK, 2018) Dir: Sandi Tan (9)

Time (US, 2020) Garrett Bradley

The Rescue (US/UK, 2021) Dir: Elizabeth Chai Vasarhelyi & Jimmy Chin

Fire of Love (US/Canada, 2022) Dir: Sara Dosa

No Other Land (Palestine/Norway, 2024) Dir: Basel Adra, Hamdan Ballal, Yuval Abraham & Rachel Szor

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