I was Googling around and put in the search terms "feminist mysteries," expecting to get back a list of books by women writers or books featuring female protagonists. Instead, what I got were links to a series of books about the neo-pagan movement, some of which I've read (Drawing Down the Moon) and some of which I haven't (The Holy Book of women's Mysteries: Feminist Witchcraft,Goddess Rituals, Spellcasting and Other Womanly Arts).
That search led me to this excerpt from a paper on occult crime and law enforcement by a writer named Isaac Bonewits. (The website is holysmoke.orghttp://www.holysmoke.org/ which turns out to be a Scientology site.)
The Physick Book of Deliverance Dane by Katherine Howe, a contemporary woman discovers she's heiress to a tradition of healing that goes back to the Salem Witch Trials and an ancestress accused of witchcraft. The book is a historical novel first and last, but it has a theme that you see over and over in witch books--a woman inherits a supernatural destiny. And in all of these books, the heroine is a strong woman, powerful and in command. (And usually beautiful, which is in itself a sort of power.) The only exception I've seen is Anne Rice's "Mayfair Witches" books, which have, to me, an unpleasant undertone of victimization and sexual politics.
Witches are empowered and sometimes they use their powers for evil. There's the Witch of Endor who raised the shades of the dead and Morgaine le Fay who lay with her own brother and begot Mordred, therefore bringing all sorts of problems to Camelot.
I always thought Morgaine was way more interesting than Guinevere. And I always thought Marion Zimmer Bradley's feminist take on the Arthurian myth (The Mists of Avalon) was one of the best out there, although I am very fond of Mary Stewart's Merlin books.
Among contemporary books about witches, I really like Kim Harrison's Hollows series. The first is called Dead Witch Walking and it is not your usual urban fantasy fare. Her heroine, Rachel Morgan, is strong, smart and sexy even though the cover art makes her look like just another supernatural babe with a tramp stamp. Other series with strong witch characters include James Clemens' Wit'ch Fire books and Deborah Harkness' All Souls Trilogy (yes, Discovery of Witches was all over the place, but wasn't it fun to read?). Some people like the James Patterson witch books, but I'm not a fan.
It's no accident that we're starting to see fairy tale mashups with noir--yesterday's witches are todays femmes fatales.