The Running Gag with Tom constantly mispronouncing "aeronaut" as "aronort", despite Becky's attempts at correcting him. He STILL hasn't learned how to say it properly by the climax of the film when the characters give themselves cool titles while chasing the comet down.
The movies versions of Cain and Abel. No sibling murders, but Cain is a leather dressed biker hoodlum, and Abel is a literal boy scout. Adam remarks that "Abel is a good boy, but if Cain had remained a bear, it would have improved him." Adam had operated under the assumption that Cain was some sort of small bear during the majority of the boy's childhood. Fridge Brilliance if you remember that Adam was never a child himself, the only other human he's ever met is Eve, and he has no idea what these whiny little things Even keeps finding are, or where they come from. At one point, Adam embarks on a journey to discover where Cain came from, leaving behind Eve who is heavily pregnant again, meaning of course that when Adam returns from his fruitless journey non the wiser, Eve has "somehow" managed to find ANOTHER child.
Adam: *exhausted* Of all the luck... *passes out in his cart*
When God first creates Adam in the Garden, Adam is sleeping, and God tries to wake his creation up.
Adam: *mumbles sleepily*
God: ADAM!! *a giant live-action hand pokes Adam awake*
God: It's for you. *meaning the Garden and all creation*
Adam: *picks up a banana and holds it like a phone* Hello?
Eve's insistence at naming things in the Garden, which she does by nailing signs to everything, including Adam. When Adam tries, he accidentally nails a sign to an elephant and gets tossed into the trees for his troubles.
Mark Twain has the kids dump as much unnecessary weight from the airship as possible. When Huck pushes out the type setter, Twain calls it the "worst damn investment he ever made".
The bit with Captain Stormfield arriving in the wrong heaven intended for an alien species. Its basically a loud, hedonistic nightclub, far too intense for a Christian man from the early 20th century. He finally finds his way to Earth's Christian Heaven, much to his relief, only to discover it might not be so great either.
Stormfield: *after being given his wings, halo and a book of hymns* Show me a cloud! I'm all right now—
Stormfield: ...I think...
Mark Twain: A harp, a hymnbook and wings?! Good god, what a swindle.