Huh... Princess Mononoke is the one I have at the bottom of my likes list. It was an okay film, I just remember watching it on Cartoon Network that one March where they aired four Miyuzaki films on consecutive weeks, Mononoke second, and I kind of felt somewhat lost storywise.
Spirited Away is the one I have at the top, it was the first, and you tend to always associate specialty with "firsts".
Howl's Moving Castle would be second, looking back on it I can appreciate similarities between Howl and Jareth—thanks in part to RedPiggy's fandom cross-universe.
Nazica (SP?) would be third. That one evoked memories of Jana of the Jungle and Ángel, a Spanish-language animated series about a girl searching the world for the flower of seven petals and scents, each petal and scent of each of the seven colors of the rainbow.
Lapeuta comes in fourth... And Kiki's Delivery Service is fifth, I thought the second half suffered when Phil Hartman no longer voiced her cat familiar.
Just my 2¢.