1) Sonny's murder as he coughs and chokes on his own blood and then finally gets out of the car only to be almost cut in half and die screaming. It was a very brutal scene, made more so by its abruptness and finality. Sonny did a lot of things wrong but it was always kinda poignant to me that he died on his way to try to protect his sister.

2) Michael's murders of Sollozzo and McCluskey when he literally can't hear anything that Sollozzo is saying. It's almost as if he's taking one last chance to still be a "civilian" and then it's all over.

3) The garden conversation between Michael and Vito in which Vito tries to find the words to apologize to Michael and Michael graciously refuses the apology. In its own way I thought that was a pretty good father-son moment. Vito probably didn't want Michael to be what he became but it was also obvious that Vito always thought Michael was the one.