The film opens with Indy braving death traps, scary spiders, waves of angry natives trying to kill him, and he pretty much takes it all in stride. Get him on the plane with a snake as a fellow passenger, though...
Indy: There's a big snake in the plane, Jock! Jock: Oh, that's just my pet snake Reggie! Indy: I hate snakes, Jock! I HATE 'EM! Jock: Come on! Show a little backbone, will ya?
The scene of Indy facing down a mean sword fighter in the Cairo market. The Mook spends two minutes twirling the blade menacingly, after which Indy makes a "I don't have time for this" face, pulls out his gun and shoots him.
Better: that look on Indy's face is actual pain from the dystentery that forced the "just shoot him" moment in the first place.
Even better than that, the natives swooping in on the Mook's corpse and stealing his sword, cheering enthusiastically.
Sallah: Asps. Very dangerous. (taps Indy on the shoulder) You go first.
Most anything Sallah says or does is pretty good for a laugh.
Indy stealing the uniform of the Officer that questioned how badly the first uniform he stole fits him.
Blink and you'll miss it, but you can actually see Indy sizing up the officer, trying to see if his clothes are the right size before knocking him out.
The DVD special features have some utterly hilarious footage of Spielberg chastising one of the snakes from the Well of Souls scene after discovering that, being cold blooded, snakes actually like to be close to fire. "You like fire? But it says in the script that you hate fire. Why do you like fire? You're ruining my movie!"