Firstly, you'll notice I've only really listed the heroines from Miyazaki's films. That's simply because he is known for making strong heroines in his films due to his feminism so it's a central element to Ghibli films. If you want to choose different heroine from another Ghibli film just go for the 'Other option'. I've also only listed protagonists.
Also, use spoilers if you're going to give away any plot, though there's not really any excuse for people to have not seen these films
For me it has to be Mei from My Neighbour Totoro. She is amazing. Dat cuteness and bravery of hers.