You should also ask whats your favorite anime based game cause Mine favorite anime game is Jump Super Stars!
Nausicaä of the Valley of the Wind
Laputa: Castle in the Sky
My Neighbor Totoro
Kiki's Delivery Service
Princess Mononoke - probably my favorite
Spirited Away - second favorite
Howl's Moving Castle
Akira
Steamboy
These are probably my favorite anime movies.