If you only consider animated feature films directed by miyazaki then:
1. Spirited away - my favorite
2. Ponyo - we were all like "wth

" during the rogue wave scene. Great animation.
3. The wind rises - epic animation during the earthquake scene. It was based on a story of a real life japanese aircraft engineer/designer during the WW II. I highly recommend this film.
4. My neighbor totoro - fun film!
5. Princess mononoke
Films i have yet to see: castle in the sky, kiki's delivery service, porco rossi, howl's moving castle
But if we consider all the Studio Ghibli films then i suggest : whisper of the heart, grave of the fireflies, from up on poppy hill, * the tale of princess kaguya *, the cat returns and nausicaa of the valley of the wind.
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