Ken Burns and Errol Morris are probably my favorite American documentarians.
The Civil War was great. Jazz is 10 episodes (about 2 hours each?), and was enough of an investment in time that I put it off for a long time, but once I started, found it riveting, and have watched like 3-4 X. Not everybody loves it, but I know of no doc on the subject with comparable scope. Probably my favorite doc, period, but I admittedly like jazz a lot. Haven't seen his baseball doc, completing the American Experience trio.
Thin Blue Line came immediately to mind. It kind of blurred the lines between doc and dramatization/re-enactment, and was I think influential in terms of structure. The interrotron was another innovation, which allowed Morris to carry on a conversation with the subject through the camera lens. Gates Of Heaven may be his greatest work. Ostensibly about a pet cemetery, something else emerged in his interviews with the family that owned it (sometimes what a movie ends up being is something different than what the director originally envisioned). Ebert championed it as one of his 10 favorite movies in any genre. Interestingly, one documentary led to another (see below). I also like his doc on Stephen Hawking titled A Brief History Of Time (same as the physicist's best selling non-fiction book).
Werner Herzog Eats His Shoe was an extra on both the Criterion editions of Les Blank's Burden Of Dreams as well as Gates Of Heaven by Morris
https://en.wikipedia.org/wiki/Werner_Herzog_Eats_His_Shoe
Conversation between Herzog and Morris
http://www.believermag.com/issues/200803/?read=interview_herzog
Ebert was a big fan of both Herzog and Morris. As noted above, Burden Of Dreams* is a fascinating look at the making of Fitzcarraldo in the Amazon jungle - the highlight is moving an actual ship over a hill/mountain to get it to the Amazon River (fraught with problems, somewhat parallel to harsh, remote location shoots by Coppola with Apocalypse Now [[leading to yet another doc]], Friedkin with Sorcerer and Herzog a decade earlier with the film Aguirre, The Wrath Of God '72 - the latter had some hilarious anecdotes, such as when fellow nut job Klaus Kinski threatened to walk because he couldn't take it any more, and Herzog allegedly pulled a gun on him and threatened to straight up murder him if he did, which I found completely believable, given the principals
). Grizzly Man, also noted above, was compelling, sad and tragic. Hopefully not too much of a spoiler (somewhat like a Columbo episode, you quickly find out how things will end, that isn't in question, but it is about how they get there), but Herzog urged a close friend of the deceased to never listen to the tape that contained the final moments of the couple. IMO it gave a rounded view of the subject, and seemed to sympathize without glamorizing him, and noted how unfortunate it was the girlfriend had to go down with him.
For All Mankind* - On the Apollo lunar missions, great, at times spooky and ethereal score evoking the vastness, emptiness and weightlessness of space by Brian Eno, all the living astronauts that set foot on the moon or were involved in those missions (as far as I can recall) in their own words, but IMO in a great artistic and editorial choice with no talking heads-type interviews that would break the mood, all spoken over NASA film, reportedly cut down from over SIX MILLION FEET (!!!) of raw film footage, and 80 hours of interviews. One of the best docs I've ever seen, very highly recommended.
List of Top 100 Docs from Rotten Tomatoes
http://www.rottentomatoes.com/top/bestofrt/top_100_documentary_movies/
Without commenting on the sequence/rankings, Man On Wire was indeed excellent. So was Jodorowsky's Dune. Fascinating how influential this aborted mid-70s project was on future sci fi films, such as Ridley Scott's Alien (visionary bio/mech hybrid artist Giger, who famously did ELPs Brain Salad Surgery cover, collaborated first here before Alien in '79), partly because the incredibly thorough visual document and mapped out story board "book" made the rounds to virtually every studio in Hollywood. Lynch didn't complete his version until '84. When original source material author Frank Herbert visited Chilean/French director Jodorowsky in '76 (avant garde and underground/cult film pioneer earlier made "acid western" El Topo '70, which led to fan John Lennon partly financing The Holy Mountain '73), the telephone book-sized script projected to a 14 hour film, after talking to Tangerine Dream and Gong for scoring he settled on Pink Floyd and Magma and it was to star an international and multi-media cast including Dali, Orson Welles, David Carradine and Mick Jagger.
Arguably the GMNM (Greatest Movie Never Made). Again, very highly recommended.
https://en.wikipedia.org/wiki/Jodorowsky%27s_Dune
Music-related
Gimme Shelter (arguably the greatest music doc ever?), on the Stones and the Altamont tragedy - the Stones In Exile was also interesting, as that was close to the epicenter of my favorite era, albeit a short doc, about 60 minutes, not counting extra interviews
Pink Floyd: Live At Pompeii (also A Technicolor Dream about the foundational Syd Barrett years and "Swinging London" psychedelic backdrop)
Monterey Pop Festival (by Pennebaker, who also did Don't Look Back by Dylan which I haven't seen, and Ziggy Stardust, which I have and liked a lot, though the visuals are flawed, but great music by Bowie, in his historic last concert with the Spiders From Mars), great footage of Hendrix and Otis Redding, among others
Woodstock
Beatles Anthology (another candidate for my all time favorite doc in any genre, along with the Jazz doc 10 part series by Ken Burns), The First U.S. Visit AND Let It Be, middle doc by the Maysles bros, who also did Gimme Shelter
George Harrison: Living In The Material World (nearly 3 & 1/2 hours, Scorcese took about a half decade meticulously researching and assembling based on countless interviews, video/film/audio elements with full access granted to his official archives by his widow Olivia, finishing in parallel while shooting Shutter Island, won several Emmys, including best director)
Lennon NYC (from the PBS American Masters series), also Gimme Some Truth: The Making Of John Lennon's Imagine album and Imagine: John Lennon, a separate doc/bio
Jimi Hendrix ('73), the recent Hear My Train A Comin (also from the PBS American Masters series, and an Emmy winner), Band Of Gypsies: Live At The Fillmore East (won a Grammy), Jimi Plays Berkeley and Jimi Hendrix: Electric Church
The Song Remains The Same
Stop Making Sense* (on Talking Heads, by Silence Of The Lambs Jonathan Demme)
Standing In The Shadows Of Motown (on the largely anonymous but brilliant musical aggregation dubbed the Funk Brothers, including legendary bassist James Jamerson)
David Bowie: Five Years
The Wrecking Crew (secret weapon on hundreds of hits from mid-60s to early 70s, perhaps most notably on The Beach Boys Pet Sounds, but Sinatra and everybody)
Blue Note: A Story Of Modern Jazz*
Respect Yourself: The Stax Records Story*
Wattstax
The Last Of The Blue Devils* (on the intersection of Kansas City blues and jazz best exemplified by Count Basie, some great background, interviews and live performances)
Thelonious Monk: Straight No Chaser on the seminal bebop piano architect (with Bud Powell) and maybe the most important composer in the history of jazz after Duke Ellington, who had like 2,000 compositions over more than a half century. Exec produced by jazz buff Clint Eastwood, directed by Charlotte Zwerin, who co-directed Gimme Shelter with the Maysles bros.
Satchmo and Celebrating Bird, on the lives and music of legendary, iconic, historically pivotal jazz artists Louis Armstrong and Chalie Parker, respectively (written and co-directed companion to two books by possibly the greatest living jazz critic, Gary Giddins - his breadth/depth of more wide ranging general knowledge evident on his commentary track for Kubrick's Paths Of Glory, as well as many Criterion essays, entrusted with some of the most important classics in world cinema, such as Bergman's The Seventh Seal and Fellini's La Dolce Vita)
Ornette Coleman: Made In America (the most important and influential avant garde jazz artist in the 20th century?)
Sun Ra: A Joyful Noise (George Clinton's whole P-Funk Afronaut vibe and elaborate cosmology/ethos was basically a career long homage)
Stranger: Bernie Worrell On Earth (just found out he is battling a late stage liver/lung cancer diagnosis and is forgoing chemo - thought and prayers extended out in all directions with maximum velocity throughout the Woo-niverse), about the Herbie Hancock-like childhood classical prodigy, secret weapon, X-factor, neglected genius and key architect of P-Funk's enduring success, who as Mos Def trenchantly noted, not only made cutting edge, state of the art sounds as a synthesizer pioneer, as others have done that before and since, but created entirely new syntaxes and SOUND WORLDS for funk - see Flashlight)
Rush: Beyond The Lighted Stage
Genesis - Sum Of The Parts
Muscle Shoals
The Last Waltz
Different Kind Of Blue (on Miles Davis fusion period)
Year Of The Horse (on Neil Young, I think directed by Jim Jarmusch?)
Buena Vista Social Club (Cuban music scene, with Ry Cooder, directed by the great Wim Wenders)
Finding Fela (about Afrobeat creator)
Making of Dark Side Of The Moon, Wish You Were Here AND The Pink Floyd And Syd Barrett Story
Several titles in the VH1 Classic Albums series (some favorites include Floyd's DSOM above, Rush - 2112/Moving Pictures, Steely Dan - Aja, The Jimi Hendrix Experience - Electric Ladyland, John Lennon/Plastic Ono Band, Peter Gabriel - So, Grateful Dead - Anthem Of The Sun and American Beauty, Frank Zappa - Apostrophe/Over-nite Sensation, The Doors on their eponymous debut, etc., etc., etc.)
https://en.wikipedia.org/wiki/Classic_Albums
40 Greatest Rock Docs by Rolling Stone
http://www.rollingstone.com/movies/lists/40-greatest-rock-documentaries-20140815/the-last-waltz-1978-20140815
* For All Mankind (in eight parts)