After retrieving the stolen treasure, Captain Flint/Uncle Jim carves a fish out of a piece of wood, writes "honesty is the best policy" on it, and puts it where the treasure was, so the thieves will get a shock when they come to find the treasure.
When the Swallows return to Wildcat Island after winning the war, the Amazons tell them about their plan and how it went wrong.
Nancy:[about their reactions upon seeing the Amazon gone] Then we had a bit of an argument.
Peggy: A bit? It was a whole one and a half.
John uses the agreed-upon signal (owl calls) to tell the Amazons they're ready to leave. Unfortunately, he does this twice, in the middle of the day, while the Amazons' Great Aunt is within hearing range. Hilarity Ensues.
Every reference to Timothy, especially the fact that the Amazons, thinking he's an armadillo, have made a wooden box for him to live in, becomes Hilarious in Hindsight after the reveal that Timothy is: 1., human, and 2., Squashy Hat.
The Picts and the Martyrs
Nancy roping various people into helping her uphold the pretense that the Ds aren't visiting. It results in the doctor telling her he wishes she was at the bottom of the sea, and Timothy saying that he'd like to wring her neck.