Little Vito singing the song about the donkey when he's quarantined. I remember my grandmother singing that song.

When all of the immigrants come out onto the deck of the ship to see the Statue of Liberty as the music swells, very moving.

The dirty look Kay shoots Michael right after the assassination attempt. It's a miracle he doesn't burst into flames right on the spot.

The scene between Fredo and Michael in Cuba, when Fredo confesses that he always felt like an outsider.

In Godfather III, when Michael kneels at Don Tommassino's coffin and asks why he was so loved when Michael was so hated. I always thought he was, on some level, speaking to Vito.