Pretty much all the Miyazaki ones - Spirited Away, Kiki's Delivery Service, Princess Mononoke, Howl's Moving Castle, etc. - have strong female characters. And they're really good movies that adults can enjoy as much as kids.
Other movies my daughter has loved (that aren't necessarily "girl" movies) include Back to the Future, Avatar, The Secret of Roan Inish, and Star Wars.
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