A few off the top of my head:

Clemenza drinking from the jug of wine, and the parallel scene in GFII with Pentangeli drinking from the hose.

The lighting on Michael when he interrogated Carlo.

Clemenza's gruff tenderness toward Michael before the Sollozzo assassination ("We were all proud of you...your father, too.").

Michael's glance at his steady hands after lighting Enzo's cigarette outside the hospital.