Without a doubt, Michael and Vito having their talk in the garden. Vito understands what his son sacrificed for him and the family, and I beleive it is his one regret, that Michael had to step in. Michael's love for his father shines so brightly in that scene, it is one of the most touching and beautifully acted scenes in the trilogy.

In II, the scene with his mother, when he is worried about losing his family. In the flashacks, almost every scene with young Clemenza makes me laugh. As for drama, the scene with Fredo in the boathouse.

In III, I love the scene when Michael confesses to the priest, and also when he kneels at Don Tommassino's coffin.