Holly Short (Artemis Fowl series, by Eoin Colfer)Read about another entry on the list.
Holly is Artemis’ best frenemy, and becomes the main female protagonist of this series. Her relationship with Fowl starts off a little rocky, what with his kidnapping her and trying to extort the Fairy People for ransom. But as the story gets more complicated, so too does her partnership with Fowl, right up until the wonderfully meta ending.
See Eoin Colfer's top ten list villains in fiction.
--Marshal Zeringue