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The Gods' brawl over who gets to carry the sun commented on as an overexcited horse race/rugby match.
It's noon! It's noon! Nooooon!
..."Why are you yelling into a bulrush?"
The amicable Ephebe and Tsort soldiers, who return to their respective sides... only to turn back and give each other embarrassed looks once they realize they went the opposite way.
The Plague of Frog, described near the beginning of the book.
It was quite a large frog.
The sequence where Pteppic's Token Religious Teammate goes to "say his prayers" before bed and some of the other kids make fun of him, only for him to drag in a goat and conduct a rather elaborate sacrifice. This leads to increasingly more bizarre rituals from every student until the headmaster has to put his foot down. Sadly, none are the actual reason no student is allowed to keep a crocodile in his room.
Dios has a persistent habit of calling Teppic "we" which leads to this gem:
Dios: It is time to raise the subject of our marriage.
Teppic: Well, I'm sorry, but I don't think we'd be compatible, Dios.