For the anime movies, I think Ghibli Studio are the best. Castle in the Sky, Pricess Mononoke, The valley of the wind... all of them are great. Personally I didn't like Spirited Away and more than likely I wouldn't like the Howls Moving Castle either, but that's just because they are not my kind. I can recongnise they great though.
The grave of the fireflies and Barefoot Gen also are great movies, althought really depressing (specially the first one).
As for Evangelion, Ghost in the Shell or Knoking on the heaven's door (Cowboy bebop), yeah, they are fine, but I wouldn't class them as great.