I think Spirited Away is very easily the best movie (of those that I have seen, of course). Both Akira and Ghost in the Shell have too many points detracting to even compete with the Ghibli movies. Howl's Moving Castle was deeply flawed (especially the ending), and the protagonist of Princess Mononoke is too boring. Whisper of the Heart and Porco Rosso are both brilliant, but a little too narrow. Spirited Away, on the other hand, is perfection.
As for series, the question is slightly more difficult. There would be a contest between Haibane Renmei and Wolf's Rain.