Any "special" chapter in which the author talks to you.
So, so many tears of laughing came from Book 3 when Yo-Yoji is a samurai and is speaking in Japanese, slicing his way through the jungle in the zoo.
"Books can also provoke emotions. Emotions can cause you to do things you'll regret, like, oh, throwing a book at someone else."
"Maybe you don't actually sing 'la la la,' but you know what I mean."
The incredibly lemony narration. Anything you might take for granted in a normal book (chapter numbers, footnotes, endings) will probably be played with in some fashion. For example, in the second book, he reverses the order of the chapters (starting with Chapter 34 and ending with Chapter 1) because he hopes the book (and the secrets contained within) will explode like the countdown timer on a bomb.
The chapters are even better in This Isn't What It Looks Like, where we have, alongside the normal chapters, negative chapters for Cass and what she's doing in the past.