I agree with most of the ones mentioned here. So I'll throw out five that I haven't seen mentioned.

1. Mr. Death
2. One Day in September
3. Ken Burns' Jazz
4. Woodstock
5. Hands on a Hardbody

An honorable mention goes to "Touching the Void," although I can seem if some quibble about classifying it as a strict documentary.

Speaking of where is that documentary on DVD, how about "Heart of Darkness: A Filmmaker's Apocalypse"?

Hearts and Minds
Bowling for Columbine
Roger and Me
The War Room
A Personal Journey With Martin Scorsese Through American Movies

Sherman's March
Roger and Me
Salesman
Dark Days
Fog of War
Bowlinf For Columbine

Here are some of my favs:
Tokyo olympiad
Monteray Pop
Salesman


One of my favorites is a little known film narrated by Richard Dreyfus, called Johnstown Flood. It also has one of my favorite covers.

http://images.amazon.com/images/P/B0...1.LZZZZZZZ.jpg

for all mankind and winged migration (if this can be called a documentary) are my favs.

My Fave DVD Docs, the ones I can watch over and over:

Best-sounding: Gimme Shelter -- Stones at their peak, DTS, and a terrific 44 page booklet. (I wish more companies would go the booklet route; I much prefer them to text-based "special features.")

Funniest: American Movie -- The commentary's almost as funny as the film itself. My favorite moment: the debate over the song "Was I Going Insane."

Best-looking (especially on a widescreen): BARAKA -- Unfortunately, after seeing this, Koyanaquatsi just isn't as impressive as it once was; not-so-great DVD transfer partly to blame there, I suppose.

Most sickening: WACO the Rules of Engagement (at least until we get F911) -- Required viewing for all Americans.

Best DVD with lots and lots of birds: Winged Migration. (Now does anyone know what the hell happened to Microcosmos?)

All-Around Coolest: Crumb -- Terry Zwigoff rules. I'd love a sequel. What's Crumb been doing in France all these years?

Seems most of us have pretty smiliar lists. Does anyone wanna recommend some obscure or forgotten titles?

I wouldn't be able to keep it at 5 so here's some I haven't seen mentioned.
Weather Undeground
Lost in La Mancha
9/11: The Filmmakers' Commemorative Edition
Keep The River On Your Right
Scared Straight!

and some others :)
startup.com
Do You Believe In Miracles?: The Story Of The 1980 U.S. Hockey Team
Ghosts Of The Abyss
Home Movie (not great but ok)
The Awful Truth (tv)
Rocked w/Gina Gershon (tv)

I agree with many listed here but here's a couple not mentioned yet... if I missed the mention, sorry...

Step into Liquid
Standing in the Shadows of Motown (This one is GREAT)

Off the top of my head:
Style Wars
Blue Planet Boxed Set
Dogtown and Z Boys
Triumph of the Nerds
Beatles Anthology

My fav's

Step into Liquid
Winged Migration
Bowling For Columbine
Touching the Void
The Kid Stays in the Picture

And I don't know if its on DVD but I saw a Documentary called "Relentless: A Stuggle for peace in the Middle East" that is about the palistinians and isrealies. It was clearifying and eye opening.

Second both Bowling for Columbine and the Kid Stays in the Picture

Shoah
Grey Gardens
When We Were Kings
Ken Burns' Civil War
American Movie;)

In no particular order:

Jazz
Bowling For Columbine
Endless Summer (if that counts as a docu)
Spellbound
The Hunting of the President (not out yet but I got a screener, so I say it counts)

Sorrow and the Pity
Grey Gardens
Tokyo Olympiad
Night and Fog
Nanook of the North

Ken Burn's The Civil War, Baseball, Jazz
Tokyo Olympiad
Cosmos
History of Soccer by Shout! Factory

Werner Herzog's Little Dieter Needs to Fly.

For All Mankind
Night and Fog
Trinity and Beyond
Winged Migration
Super Speedway Mach II SE (the DTS rocks :))

Ken Burns Civil War
Walking With Dinosaurs (plus all companion discs)
Ghosts of the Abyss
A&E TITANIC
IMAX Mysteries of Egypt
Las Vegas


Pseudo Documentaries:

From The Earth To The Moon
Band Of Brothers

Although movies or mini-series, these are so strict to historical fact and include additional historical information I classify these with my documentaries

When We Were Kings
Bolwing For Columbine
Roger and Me
The Fog of War
War Room

Top of my head...

Stoked: The Gator Story
Bowling for Columbine
Pornstar: The Legend of Ron Jeremy
Miracle
Name escapes me, but the Doc of Holmes found on Wonderland as a bonus.

They Might Be Giants-A Tale Of Two Johns
Straight, No Chaser
Chuck Jones - Extremes and Inbetweens
Bowling For Columbine
Woodstock

Here's are some of the best ones I've reviewed for DVDTalk:

Shoah
Muhammed Ali: The Greatest
The Specialist
Keep the River on Your Right
Scratch
Tokyo Olympiad
New York: A Documentary Film
Grey Gardens
Gimme Shelter
Paul Taylor Dancemaker
Jackie Chan: My Stunts
A Great Day in Harlem
The Filth and the Fury

Spellbound
Lost in La Mancha
Roger and Me
Bowling for Columbine
Full Tilt Boogie