There are many priceless, subtle moments. Brando's hand gesture, signaling Hagen to get Bonasera a drink right at the beginning, was worth an Academy right there. So was his gesture to Hagen to leave his chair alone at the Don's convention. And the way Brando made his face rise and fall when told of Sonny's death, and when telling Bonasera, "Look how they massacred my boy!." All wonderful.
Another subtle moment: Michael on Roth's hotel room terrace, smiling humbly when Roth says, "The doctors would disagree [about Roth's prospects for living], but what do they know," when Michael is planning all along to kill him.