Most of DWJs books have strong female protagonists. Or, in the case of Charmed Life - baddies. 
In addition to the ones mentioned by LRD I'd add:
Wilkins' tooth (the baddie is a woman and she is very bad indeed but there are many strong female characters among the 'goodies' - and it's the female characters who save the day);
The Merlin Conspiracy (the two main protagonists are equally gender balanced which seems fair to me)
The Sword of Dalemark (this is a sequel to the Dalemark series, The Spellcoats was mentioned above, although that was the third book in publication order it is chronologically the first book. The middle two do have some strong women characters but actually are perhaps the least feminist of all her books.
The Time of the Ghost - all the main protagonists are female.
Fire and Hemlock - again, the main protagonists (both good and bad) are female although there are some strong male characters in this one too
The Game - another young female protagonist
8 Days of Luke - gender balanced protagonists - the female 'lead' is a bot of a wimp to begin with but becomes proper good (role model wise) at the end
The homeward bounders - the main protagonist in this is male. But there are some really excellent female characters too, and they are very kickass
Basically DWJ is the greatest writer than ever lived. I reckon. 