In no particular order...

Maleficient, Cersei Lannister, Hela, Bellatrix Lestrange, Cruella, Ursula, Queen of Heart, Poison Ivy, Wicked Witch, Mom from Futurama, not sure of the xenomorph queen from Aliens counts?, GLaDOS, Number Six, Stargate had a few over the years, Starcraft's Kerrigan/Queen of blades, Resident Evil's Lady Dimetrescu, Carmen Sandiego, Doom's Olivia Pierce, Airbender's Azula, Carrie, Annie Wilkes from Misery, Claire from House of Cards, the Aunt in Handmaiden, Harley Quinn, Lady Macbeth...

That's all I have for now

One stereotype to avoid (or lean into, lampshade, or subvert) is that villainous women are manipulative, seductive, using guile, deception, charm, enchantment and so on. Your basic Poison Ivy template. Even Catwoman is sometimes depicted that way (like in @neilhimself's "Whatever happened to the Caped Crusader", albeit in a reference to "The Death of Robin Hood").

I'm personally kinda a fan of the trope and Ivy is my fave Batman-verse character but speaking to a lot of other women I know it's something many are sick to death of. Especially when that seems to be the only kind of villainous woman. (Just like how chainmail bikinis became less of a problem when it was just one of many styles and not the only option.)

I see that a lot of other examples in the thread immediately went for that trope and I don't blame 'em—only goes to show how pervasive it is and how refreshing some other approaches would be.

Few top of my head

• Poison Ivy (DC Comics)
• The Dathomir witches, especially the Nightsister clan (Star Wars)
• Number Six (Battlestar Galactica)
• Hela (Marvel)
• Cersei Lannister (ASOIAF)

But that said often you can just take a male villain and change them to a woman. Or non-binary. Would it be anything diffrent if it was EMPRESS Palpatine? LADY Vader would change a few things, but imagine on Mustafar Anakine being late in pregnacy. Duel with Kenobi plays out and she is left legless. Then waking up and being told "in your anger you killed them". Oh the self-loathing and hatred towards kenobi. Dammit I need dark-as-frakk Lady Vader fanfic now.

Check out rejectedprincesses.com, it has a great collection of powerful women. Not all of them are "bad", per se, but many of them are; there's a whole collection of female criminals for example. Or you can just use the "personality" search on the sidebar.

Cruella DeVille, Ursula, Poison Ivy

For D&D I can also think of Lolth, Tasha//Iggwilv (depending on your interpretation of that mixed bag of lore threads), Ravel Puzzlewell (a hag so powerful or madly knowledgeable she has aspects across the planes from the Planescape setting), and Loviatar the Mistress/Goddess of Pain.

There's also existent queens like Queen Mary("Blood Mary") that oversaw religious purges that you could take inspiration from. (Zealots are rarely reasonable enough to be bargained with.)

You could also just take a historically male example and invert the sex and not make a deal about it. See if your players even notice.

Read any Anita Blake books by Laurell Hamilton? There are some good female bbegs in that. The first 10 are incredible but after that the mystery aspect gets squeezed out by sex and relationship angst and they get increasingly worse.

Honored Matres from Dune?

Some good inspirations:

Master Cyclonis from Storm Hawks is basically what happens when you put personality of generic evil overlord into a body of snarky teeenage goth girl. She has a tendency of putting people off in a "expected someone taller" way.

Arcane actually has a lot of interesting female villains, with Jinx as a villain protagonist on a downward spiral, Sevika as a ruthless, but loyal criminal enforcer and Ambessa Medarda as a cutthroat politician.

Avatar: the Last Airbender, has, of course, Azula, who is damn good complex character.

Lady from the Chronicles of the Black Company is one of best written evil overlords in fantasy genre.