DC, you flatter me!
The happiest contest in the world is trying to determine the "best" or "favorite" scene in the trilogy--no losers!
That said, the scenes that I've watched (literally well over a thousand times each since 1983 (when the "Saga" was first shown on TV, and I bought my first VCR to tape it) are:
--Connie's wedding: specifically the opening with Bonasera. Vito crooking his finger to Hagen to get Bonasera a drink was worth an Oscar in itself. So was the way he puffed himself up before saying, "And then they would fear you."
--All of the Havana stuff, which is so authentic that serious professors of Cuban history tell graduate students to watch it to get a feel for what Havana was like on the eve of Castro's takover. Specifically Roth's soliloquey (watch how FFC ordered the baby spots on Roth's eyes when he says, "This...is the business...we've chosen...").
--The Don's convention; specifically Vito gesturing to Hagen to pull back his chair, and especially when he puts his hand over his heart and says, "And I swear, on the souls of my grandchildren..."
--All of the scene in Sicily with Sr. Vitelli. Another brilliantly authentic scene, and Vitelli is superb. Also notice how Pacino abruptly transitions from Michael the little lost boy in Sicily to Michael the commander.
--Almost anything with Michael V. Gazzo, who makes GFII; specifically he and Michael in the boathouse, and Michael shouting at him in his study (IMO, Pacino's best scene in the entire trilogy). Frankie playing Everyman as Caporegime: "Michael, I don't have your head for the, the big deals..." And yes, the prison yard with Hagen, and that final, soft, "See ya, Tom..." Another Oscar right there.

I'm running off at the mouth (as usual). Gotta stop...