Hmmmm, that's a toughie. Spirited Away, Princess Mononoke, Howl's Moving Castle and Castle in the Sky are all among my favourite films. Castle of Cagliostro (gee, Miyzaki sure had a thing for castles) was very enjoyable to watch as well, especially because one of my favourite games, Sly 2: Band of Thieves, bears quite the resemblance to it in some ways. If I had to pick just one though, I'd probably go with Princess Mononoke, but they're just all so lovable.
Grave of the Fireflies deserves a mention too. It's one of those movies that was superb, but I don't want to watch it again because it would depress the shit out of me and probably make me cry just as hard as when I watched it for the first time. Which was pretty damn hard.