Spirited Away, followed closely by Howl's and Princess Mononoke. Those are the triumvirate, in my opinion. But there isn't one I don't love. It's amazing watching Ponyo and Totoro back to back. They could have been made at the same time (barring some sharpness in the lines and colors). He's just a magician.
I recently listened to the Howl's audiobook and it's also enchanting, but Miyazaki changed so much to make it fit his worldview. Because there are never really bad guys in his movies, just misunderstood guys, and the tension is always internal. He's such a genius.