Beyond Good and Evil

American McGee's Alice

Resident Evil

Perfect Dark

Old NES Games based on the Alien movies (Ripley)

Donkey Kong Country 3 (Diddy Kong is the main character)

Chrono Trigger's main hero is a male, but 3 of the other 6 playables are strong females (2 of the others are a Frog and a Robot)

There are definitely more games with male protagonists than female, but there are enough to list.

Here's your list, starting with Ms. Pac-Man

http://www.giantbomb.com/female-protagonists/92-2287/

Final Fantasy X arguably. X 2 for sure. XII and XIII as well.

Ironically, the first games I thought of, Fallout and Elder Scrolls, are probably not the best choice for a girl who can't read yet.

Portal.

Mirror's Edge

Jill Of The Jungle

The longest journey and its sequel, Dreamfall

Pokemon