I second pretty much everything everyone else has mentioned! (But especially anything and everything by Angela Johnson, Sherwood Smith, Tamora Pierce, Robin McKinley, Shannon Hale, Nnedi Okorafor-Mbachu, and Diana Wynne Jones.)

Adding:

Megan Whalen Turner's Thief series is pretty much my favorite book series ever and I like to take every opportunity to recommend it. The Thief is the most kid-friendly, but the later installments should be fine as well and it isn't until the second book that the two queens really have the opportunity to shine. Turner's short story collection, Instead of Three Wishes, is a delight as well and very girl-friendly, though I've no idea if it's still in print.

Ursula K. LeGuin's Annals of the Western Shore, composed thus far of Gifts, Voices, and Powers. YA. Her Earthsea books are excellent, too, and I started reading them about the age of ten, so.

Nancy Farmer's A Girl Named Disaster and The Ear, the Eye and the Arm are both excellent.

Midori Snyder's Queen's Quarter trilogy, which was recently reprinted by Firebird.

Pamela Dean's The Secret Country trilogy, also reissued by Firebird.

Speaking of Firebird, the short story anthologies Firebirds and Firebirds Rising are both excellent and highly recommended.

The first book in Tanith Lee's Claidi's Journals books - Wolf Tower - remains one of my preferred comfort reads and I do recommend it. Not so fond of the later entries in the series, in which everyone behaves terribly to one another, the heroine spends most of her time moping, and most of the villains are women.

Landy's Skullduggery Pleasant books are suitable for a young age and they've loads of engaging female characters behaving awesomely on a regular basis.

Garth Nix's Abhorsen series.

Patricia Wrede's The Enchanted Forest Chronicles ought to be recommended reading for everyone in middle school.

Lloyd Alexander's stuff tends to be pretty good, but I'm most fond of The Prydain Chronicles.

Harriet the Spy by Louise Fitzhugh. I haven't read the sequel yet, unfortunately.

Sorry I haven't much else to add!