Grave of the Fireflies! Probably the BEST Ghibli film ever! It is so moving and well directed it is simply amazing. It is one of those movies that you are GLAD they didn't animate realistically, because as it stands... when you watch it you WILL cry your eyes out.... Seriously... If you haven't seen it, grab a box of tissues, sit down and watch it.
Other than that I think Princess Mononoke, Howl's Moving Castle, and Spirited Away are all fantastic.
Really, I can think of only a few Ghibli films that I didn't like, but even those have merits that deserve praise.