As said before, Duvall's facial expressions are the best. Aside from the ones already mentioned here, I think my favorites are:

The scene with Johnny Fontaine in the Don's office

The scene when Michael offers to kill Sollozzo and McKluskey

The scene in GF2, when Michael tells him Tom that he's the only one he can trust, that he thinks of him as a brother, and Tom just looks so darned grateful.

I also love Diane Keaton's eyes right after the assassination attempt in Tahoe, when she's cuddling Mary on the sofa. If looks could kill...