I'm pretty sure the only ones I haven't seen are Baron the Cat Returns and Ponyo.
Princess Mononoke was the first Miyazaki film I saw, so it will always be one of my favorites. My next favorite would have to be Howl's Moving Castle, then Kiki's Delivery Service and Spirited Away (tied).
And, no one's mentioned Whispers of the Heart. That was a cute movie.
(And, sorry, but Totoro was confusing for me.)