Oh, oh, that's pretty hard. Let's see.
#1: Nausicaä

That is practically the essence of Miyazaki-movies. he has all three main themes he makes movies about in this one: War, Flying and the relationship between nature and humans. That said, other great movies have to step behind this: Porco Rosso, Princess Mononoke, Spirited away, Howls Moving castle, Laputa, Kikis delivery service. All of them are great, but Nausicaä for me is the best of them all.
#2: Grave of the Fireflies

Well, this movie gets everyone crying. I never saw one, who wasn't touched by it.
#3: Whisper of the heart

That is such a beautiful movie. (Concrete Roads)
Well, as said before, I can recommend all Miyazaki movies and basically all Ghibli movies. These three I have to choose, if I have to reduce to three.