When Bonasera asks "How much shall I pay you?" Tom's movements afterwards, as if he's thinking "Jeez... Really?"
In II, Tom's hand gestures when he says to Geary about the dead whore: "It will be like she never existed."
The slicing of the Cuba cake; the symbolism is obvious but I love it.
In the last scene with Frankie and Hagen: Frankie's "See ya, Tom." That line feels SO real I'm sure it was improvised by Gazzo. I'm glad the editor left that moment in.