Good list. Havent seen all of them, but also dont consider all of those I have to be great. But female filmmakers are still marginalized, although a lot has happened in the last two decades.

And btw. John, you shouldnt forget to mention Alexander Hammid when you are speaking of Meshes of the Afternoon. He was a forerunner of the new wave in Czechoslovakia in the 60s, with his poetic films from the 30s. He is also at least as interesting and important a filmmaker as Deren herself - besides having taught her most about filmmaking himself. Just noticed that imdb isnt even listing all of his 30s work... :x 

On a sidenote, Im aso glad you picked Baise-moi. As you might know, only few people like that film. 

My Top 25 in chronological order with additional two that are Straub/Huillet 

Clo de 5 7 Cleo from 5 to 7 (1961 / France / Agnes Varda)
La drive (1964 / France / Paula Delsol)
Sedmikrasky Daisies (1966 / Czechoslovakia / Vera Chytilov)
Eltvozott nap The Girl (1968 / Hungary / Mrta Mszros)
Othon (1969 / West Germany, Italy / Jean-Marie Straub, Daniele Huillet)
rkbefogads Adoption (1975 / Hungary / Mrta Mszros
Voskhozhdeniye Ascent (1976 / Soviet Union / Larisa Shepitko)
Maternale Mother and Daughter (1978 / Italy / Giovanna Gagliardo)
Klassenverhltnisse Class Relations (1984 / West Germany, France / Danile Huillet, Jean-Marie Straub)
Sans toit ni loi Vagabond (1985 / France / Agnes Varda)
Rosa Luxemburg (1986 / West Germany / Margarethe von Trotta)
Sale comme un ange Dirty Like Angel (1989 / France / Catherine Breillat)
Europa Europa Europa Europe (1990 / Germany, France, Poland / Agnieszka Holland)
Ketu qiuhen Song of the Exile (1990 / Hong Kong, Taiwan / Ann Hui)
The Piano (1993 / Australia, New Zealand, France / Jane Campion)
Moe no Suzaku Suzaku (1996 / Japan / Naomi Kawase)
Verrckt bleiben - verliebt bleiben (1997 / Germany / Elfi Mikesch)
Boys Don't Cry (1999 / USA / Kimberly Peirce)
Jesus' Son (1999 / Canada, USA / Alison Maclean)
Baise-moi @#%$ Me (2000 / France / Virginie Despentes, Coralie Trin Thi)
Vendredi soir Friday Night (2002 / France / Claire Denis)
My Life without Me (2003 / Spain, Canada / Isabel Coixet)
Te doy mis ojos Take my eyes (2003 / Spain / Icar Bollan)
Marseille (2004 / Germany / Angela Schanelec)
Babooska (2005 / Austria, Italy / Tizza Covi, Rainer Frimmel)
La-bas Down There (2006 / Belgium, France / Chantal Akerman)