I LOOOOOOOOVE female villains. Nearly all the characters I write are female villains or female anti-heroes just because they're so awesome and we don't have enough of them. Some of my favorites:
1. Azula (and friends) from Avatar: The Last Airbender
Completely unhinged, but unmistakably human. Kind of a shame we never got much of a backstory for her, but perhaps it wasn't needed. Based on her family situation and the values she was raised to uphold, it makes sense she'd end up like this.
2. Kuvira from The Legend of Korra
Korra in general was a let down compared to The Last Airbender, was Kuvira was a cool villain. She was pretty much a fascist, but you could always understand where she was coming from, even if you disagreed with her methods.
3. Cornelia from Code Geass
Cornelia wasn't the final villain of the show, but she was the most visible antagonist for the first season. She was smart, strong, tough, ruthless, calculating, and had a great commanding presence while being hot as hell.
4. Homura Akemi from Madoka Magica
Becomes the devil herself and rewrites the universe just so she can have her best friend all to herself for all of eternity. Hard to beat that lol.
And that's all I got for now lol. There really aren't that many great female villains, and what few we have are more sex appeal than actual character.