My favourites:
Just before MIchael kills Solozzo.
The fury building inside of himwhen Kay tells him about the abortion.
Brando's smile when Michael tells him at the hospital " im with you now..im with you"
Brando pausing after learning that Sonny has been whacked.

Theres too many actually.....

Michael's fear when he has trouble finding the gun behind the "bucket and chain thing" in the bathroom of the restaurant.

I had to re-create a silent scene with little or no dialogue for my film class freshmen year. I chose the scene of when Michael is with the baker's son in law in front of the hospital as they scare off the hitmen who come to kill Vito. I liked this silent scene as tension was high and a lot was revealed about Michael with no dialogue. We see the son in law's hands shaking badly after the scene, while Michael's hands are calm. Michael begins to realize that he is not all that different from his father. I couldn't compete with that scene, but it was fun for me to direct the scene and my professor said I did good job as many other projects had too much dialogue in them.

Micheals walk back to office when Carlo gets strangled

The looks on the others faces when Sonny speaks out at the meeting with the Turk

Two quick moments of silence that always make me laugh:

1) The look on Woltz's face when Tom tells him to put Fontaine in
the picture. Woltz is signing something on a clip board, and he sort of looks at the guy holging it and makes a little smirk.

2) The look of utter shock on Moe Greene's face when Micahel says "Is my credit good enought to buy you out?"