Very catholic lists, John and A. I haven't seen a number of films on both your lists. Istead of zooming in on favourites (which I find rather difficult to do), I'll put down a rather long list of films I liked very much, in no particular order. My clear favourite, though, among women directors is Agnes Varda and she keeps coming back like a refrain I've seen 8 films by her so far and I am kind of bewitched my the so-called 'grandmother of the nouvelle vague'. 

Triumph of the Will (Leni Riefenstahl)
Meshes of Afternoon (Maya Deren)
The House Is Black (Forugh Farrokhzad)
Cleo from 5 to 7 (Agnes Varda)
Daisies (Vera Chytilova)
Asthenic Syndrome (Kira Muratova)
The Gleaners and I (Agnes Varda)
Blackboards (Samira Makhmalbaf)
The Day I Became a Woman (Marzieh Meshkini)
The Joy of Madness (Hanna Makhmalbaf)
Anatomy of Hell (Catherine Breillat)
The Swamp - (Lucrecia Martel)
Sweetie - (Jane Campion)
Le Bonheur (Agnes Varda)
Titus - (Julie Taymor)
Boys Don't Cry (Kimberley Peirce)
A Study in Choreography for the Camera (Maya Deren)
The Chronicle of Anna Magdalena Bach (Danielle Huillet/Jean-Marie Straub)
Fruits of Paradise (Vera Chytilova)
36 Chowringhee Lane (Aparna Sen)
Vagabond (Agnes Varda)
Kali Salwar (Fareeda Mehta)
The Lost Honour of Katherina Blum (Margarethe Von Trotta/Volker Schlondorff)
Riddles of the Sphinx (Laura Mulvey)
Sophie (Liv Ullman)
The Connection (Shirley Clarke)
Apple (Samira Makhmalbaf)
Dageurreotypes (agnes Varda)
Europa Europa (Agnieszka Holland)
Baise-moi (Virginie Despentes/Coralie Trin Thi)