For me its the scene with Sonny's body in Bonasera's funeral parlor...its one of the few times we see Don Corleone feel any sort of regret for the life he's chosen to lead. It stands in direct contrast to the scene in the garden w/Michael "I refused to be a fool..,etc."

It starts when he walks in...notice the utter numbness with which he says "Well Bonasera, are you ready to do me this service?" (the look on Bonasera's face is priceless, he's absolutely terrified) But its really when he says "Look how they massacred my boy..." that you really, I think, get a sense of guilt. There's the obvious heartbreak of losing a son...Brando's so good he only needs one line to convey this feeling. But pay close attention to Brando's facial expressions afterwards...the way he raises his eyebrows, as if he disbelieves the words coming out of his own mouth. Its as though he's thinking "'They' massacred him? I did. It's my own fault, who am I kidding." Amazing what a good actor can do with a pair of eyebrows.