I’ll admit to being slightly sexist when it comes to movie bad “guys”: I just have a hard time accepting a woman as the antagonist. Perhaps it’s that I associate villians with superior physical power, which the women in movies seldom seem to have. That’s not to say that I don’t think women can be evil or nasty in the movies; I just can’t see a female as the head heel, as it were (a female Hannibal Lecter? can’t see it). So, I’d appreciate it if ya’ll could give me the names of some movies that DO have effective female villians, so I can try and overcome this shortsightedness.
The Borg Queen comes to mind.
There is SHE, H. Rider Haggard’s antagonist.
There is probably a Holmes movie with “the woman” whose name escapes me.
Whats-her name, Mirna Loy (sp) The Maltese Falcon.
Angela Lansbury in Manchurian Candidate
Penny Johnson in 24
I believe it was Mary Astor in “Maltese Falcon”.
Sean Young in “Ace Ventura” (if I don’t get laughed off the Board for having seen that flick).
“The Intendent” in the DS-9 Mirror Universe (Star Trek, ever the innovator in the female bad guy)
Lots and lots of “femme fatale” flicks out there, like “Body Heat” (Kathleen Turner), (and “Double Indemnity” which inspired it) “Last Seduction” (Linda Fiorentino) and of course the current DePalma “Femme Fatale” movie which I haven’t seen yet. And many others.
As a general observation, movie villians often have very little physical strenght; they love to put them in wheelchairs (Blofeld), remove their limbs (Dr. No), hide them in hot-houses (“Eiger Sanction”), etc. Being a frail woman is no great disadvantage in the world of E-vil…Timmy
From Disney:
Maleficent
Cruella De Ville
Ursula
and various stepmothers
Other movies:
The Bad Seed (a little girl no less)
The Hand that Rocks the Cradle (evil nanny)
Superman II (Ursa)
Misery (Annie the obsessed fan)
That’s all that’s springing to mind atm.
“The Hand That Rocks The Cradle” had Rebecca De Mornay as a really evil bitch.
Lilith.
Delilah.
Judith.
Herodias and Salome.
Circe.
Medea.
The Bacchante.
For more, see Bram Dijkstra’s IDOLS OF PERVERSITY: Fantasies of Feminine Evil in Fin-de-Siecle Culture (Oxford, 1986).
Damn, sorry Luna I just spotted you had mentioned that already.
Instead I offer:
“Fatal Attraction” - Glenn Close played a fairly creepy psycho, though not strictly a villain in the traditional sense.
Fay Dunaway in “Supergirl.” Not the best example, of course. 
Not “Baby Jane”, but “Blanche”. A really bad, bad sister.
Oh yeah, and sweet little Patty McCormick from the movie, “The Bad Seed.” (the original) Whoa, talk about a midget-villainess. They invented the “bad girl” mold with her!
Lena Olin in ROMEO IS BLEEDING.
Miyazaki’s animated films have some fairly memorable female half-villains. Half-villains because they usually have some good points as well.
The best is Lady Eboshi from Princess Mononoke but there are others in Nausicaa, Castle in the Sky and Spirited Away.
The “wicked witch” is a standard in children’s films including Wizard of Oz and Snow White.
For a different kind of female villain see All About Eve for a terrific portrayal of a scheming,lying actress played by Anne Baxter IIRC.
Paulina Novacek from Undercover Blues.
Jessica Walter in “Play Misty for me.”
Natalie (Carrie-Anne Moss) in “Memento”
Nurse Ratched (Louise Fletcher) in “One Flew Over the Cuckoo’s Nest”
Mrs. Danvers (Judith Anderson) in “Rebecca” (although there’s some question whether she was was more psychotic than evil).
And from the various screen adaptations of Shakespeare’s “Macbeth”
-Lady Macbeth
Baroness, from G.I. Joe: The Movie. Accept no substitutes. 'Though Xenia Onatopp from Goldeneye almost comes close.
Then there’s Mrs. Haversham, from Great Expectations.
Ilsa, she-wolf of the SS ?
Phyllis, played by Barbara Stanwyck, in “Double Indemnity”.
Diana(Fay Dunaway) in “Network”.
Sadako, in the Japanese original of The Ring (Samara is her American counterpart).
Laura Flynn Boyle in Men in Black 2