A sandwich is a sandwich, but a Manwich is a meal
"Evil people can do some non-evil things, and most of them do. That doesn't mean they aren't evil." -- JeffereyWKramer
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The mysterious villain known as "The Octopus" was not a woman. Or at least he always was disguised as one man or another (but always wearing some distinctive gloves) whenever he met The Spirit, which I admit might not be the same thing as "he was really a man and a strip-search would have proved it!" But the point is that I don't recall a single hint that "he" was actually a female cross-dresser. I suspect you were getting him mixed up with one of the other colorfully-named characters from The Spirit's Golden Age stories.
But getting back to the main point of the thread . . . some of my personal favorite non-Batman-connected supervillainesses include:
Marvel's version of Morgan Le Fey.
Dark Phoenix.
DC's first Terra (Tara Markov who died in "The Judas Contract").
Marvel's Anarchy (no relation to DC's "Anarky," aka Lonnie Machin).
Emerald Empress.
Selene/Black Queen.
Marvel's Nanny (the one who had a minion called Orphanmaker).
Blackfire.
Lady Shiva.
Oh yes, and I'm rather fond of the Pre-Crisis version of Wonder Woman's old sparring partner "Dr. Cyber!"
I agree with WW
Circe
Damn how freakin underrated. She believes the amazons mission for peace with a combat society is a farce. She should be a wrecking ball in the dc universe, and a damn powerful magic user.
Cheetah(barbaraminerva) She is a dark indiana jones, also cursed by her gods so being a utter opposite of Wonder Woman. Plus with her jealousy of Wonder Woman she is a highly destructive foe.
Silver Swan
Devestation
Typhoid Mary
If we can include anime characters then I say Balalaika from Black Lagoon
Fatality I think is a great Green Lantern villainess. Star Sapphire used to be as well but she is now a hero too.
Of course, I dare. I'm Hal Jordan.