Here are some documentaries I saw and found interesting:
Japan In Colour - The Wonderful World Of Albert Kahn documentary(2009)
Kidnapped documentary BBC (2005)
Matsumoto Takako - Yayoi Kusama I Love Me.2008 documentary
Fukui Shozin - Hentai Land documentary
Low Adam - Kurosawa (2001) documentary
McAllister, Sean - Japan A story od love and hate (2008) documentary BBC4
Teenage Japanese Killers (Crime And Investigation, 2000) BBC documentary
Nemoto Masayoshi - Budo The Art Of Killing (1978)documentar>
Nozawa Kazuyuki - Haruko (2004) documentary
Limosin, Jean-Pierre - Young Yakuza (2007)
I once saw an English language documentary about Unit 731
http://en.wikipedia.org/wiki/Unit_731
I don't remember the title. I downloaded it form demonoid.com as far as I remember.