Lily quench, clementine, ronia, the girl the dragon and the wild magic, the secret unicorn (though DH read some and said it was awfully written, I'm guessing like Magic Treehouse), Celia and the fairies, Fairy Realm series, enchanted forest dragon books (Cimorene is awesome!), the girl who circumnavigated fairyland....
FYI The Dealing in Dragons that I mentioned is the first of the enchanged forest dragon books (Cimorene is awesome!) I agree she most defiantly is..
And if you haven't read them, I love many of Robert Munsch's books except for his most famous. (I'll love your forever) They aren't chapter books and a bit quirky, but they are age appropriate and many of them have a strong female main characters. For example Stephanie's Ponytail, Angela's Airplane (Annikins), The Paper Bag Princess, Alligator Baby.
