The U rated Studio Ghibli are: Kiki's Delivery Service, My Neighbour Totoro, ponyo, Howl's Moving Castle, Arriety
Other female led U rated animations: The Wild Thornberrys, Lilo and Stitch, Despicable Me has lots of female characters but a male lead, The Secret of N.I.H.M., Hoodwinked, The BFG, The Incredibles has several female charcters but a male lead, The Last Unicorn, A cat in Paris, The Rescuers, Kirikou and the Sorceress.
PG rated films: Coraline, Wreck It Ralph has a male lead but good strong females, Monsters v Aliens, Brave.
Live action films with female leads: Charlotte's Web, The Secret of Moonacre, Wizard of Oz, Alice in Wonderland, Mary Poppins, Annie, A Little Princess, The Railway Children, Nim's Island, Matilda, Spy Kids, The Chronicles of Narnia, The Princess Diaries, the Parent Trap, Freaky Friday, Nanny McPhee, National Velvet, The Secret Garden, The Fox and the child, the Secret of Roan Inish, Return to Oz.
Depending on your taste, most Disney princesses from Beauty (and the Beast) onwards make a nod at feminism but some are more acceptable than others. I like the complex mother-daughter relationship in Tangled but generally try and avoid the princess films. Lilo and Stitch is a million times more acceptable.
A Mighty Girl has a good selection of films with female leads, it's worth looking at the Bechdel Test to see if there are lots of female characters, the good thing about Studio Ghibli is the depth of the presence of women in the films.