Indiana and Marion exchanging glances at Sallah's house. You can tell they still feel something for each other despite the past.
Sallah's children/nieces/nephews coming between Indy and Belloq, just as Belloq's goons are about to shoot Indy. Calling him "Uncle Indy" the entire time. The goons are so amused by it, they allow Indy to walk out unharmed, laughing all the while.
Belloq: Next time we meet, it'll take more than children to save you.
Near the end, when Marion gives Sallah a farewell kiss on the cheek in gratitude for all his help, just before she and Indy board the ship for home. Sallah's response is even more heartwarming as he obviously wasn't expecting this. Slowly he breaks into a big, radiant smile and starts singing "A British Tar," much to the amusement of several workers nearby, one of whom Sallah gives a random, manly kiss as he continues to sing...
Indy and Marion on the ship, Marion playing doctor.
Indy: Ow! That hurt!
Marion: Well goddamnit, Indy, where doesn't it hurt?
Indy: (points to his elbow) Here. (Marion kisses it. He then points to his cheek.) Here. (She kisses it, then he points to his forehead.) This isn't so bad. (She flips his hat off and kisses his forehead. He points to his lip...)
Indy willing to destroy the ark he has been pursuing to rescue Marion
The ending, with a sharp-dressed Indy and Marion in D.C.
Indy: (referring to the government types that have just ignored everything he's said) Fools. Bureaucratic fools. They don't know what they've got there.
Marion: Well I know what I've got here. C'mon, I'll buy you a drink. (They walk off arm-in-arm.)
Indy and Marion's brief reunion after Indy and the viewers assumed she died in the truck explosion.