My tastes may seem very eclectic, but those are simply the best I have seen, and though it's not like I have seen hundreds of documentaries, these ten are (near) masterpieces that should be seen by every cineaste. Some of them are not completely "documentaries", but the term is so hard to define, and if Nanook counts, so do they. :)

1. Verrckt bleiben - verliebt bleiben (Elfi Mikesch / Germany / 1997)
2. Au-del de la haine Beyond Hatred (Olivier Meyrou / France / 2005)
3. Sans soleil Sunless (Chris Marker / France / 1982)
4. Goff in der Wste Goff in the Desert (Heinz Emigholz / Germany / 2002)
5. Les ministres de l'art (Philippe Garrel / France / 1988) 
6. Otaku (Jean-Jacques Beineix, Jackie Bastide / France / 1994)
7. Salesman (David Maysles, Albert Maysles, Charlotte Zwerin / USA / 1968)
8. Une sale histoire A Dirty Story (Jean Eustache / France / 1977)
9. Zwischen zwei Kriegen Between Two Wars (Harun Farocki / West Germany / 1977)
10. Le tombeau d'alexandre The Last Bolshevik (Chris Marker / France / 1992)

Runners up:

La-bas Down There (Chantal Akerman / Belgium, France / 2006)
Balkan baroque (Pierre Coulibeuf / France / 1999)
Babooska (Tizza Covi, Rainer Frimmel / Austria, Italy / 2005)
Pripyat (Nikolaus Geyrhalter / Austria / 1999)
One Way Boogie Woogie (James Benning / USA, Canada / 1977)
Paradjanov: A Requiem (Ron Holloway / USA, Germany / 1994)
Models (Ulrich Seidl / Austria / 1999)
La Soufrire (Werner Herzog / West Germany / 1976)
La sortie des usines Lumire Leaving the Lumiere Factory (Louis Lumiere / France / 1895)
Koyaanisqatsi (Godfrey Reggio / USA / 1983) 
Golden Lemons (Jorg Siepmann / Germany / 2003)

and I need to see again:
Khaneh siah ast The House is Black (Forugh Farrokhzad / Iran / 1962)


Btw, do concert movies count as documentaries? I'm not really sure, though I would probably count them in. What's your opinion.