Footnoted and Fancy Free
One of the peculiar delights of written English is the ability to use footnotes not just to expand the text but to connect with the reader in a way that can be unusual, personal, and very funny. The first author I found using footnotes this way was Jonathan Stroud, and over the years I've seen several authors using similar techniques to escape the boundaries of a conventional narrative. The only downside to this list is that audiobooks often lose the flavor of the author's intent so I definitely recommend the print version.
The questions in "What If?" are interesting in their own right, but Munroe's snark comes through very clearly between the stick figures and the footnotes. If you're interested in more from him, his well-known website xkcd.com incorporates alt-text on his comics as a sort of digital footnote.
Also a good one for math nerds! The teenagers in John Green's books are often a little too smart for their own good with hefty doses of self-reflection; Colin maybe needs it more than most.
Hardcore literature nerds will especially enjoy this one. Fforde clearly loves the classics and gives well-known characters their own lives outside of their original stories.
Unlike some of the others on this list, nearly everything Roach has written is extensively footnoted so try any of her books for equally amusing histories of the seemingly mundane.
Alternate historical fantasies are my favorite, but I have to say this one managed to surprise me.
Pratchett is also very well-known for his footnotes. "The Truth" is one of my favorites (and perennially relevant, it seems).
I often recommend Matthew Quick for those who enjoy John Green his work being similarly quick-witted, quirky and requiring abundant Kleenex.
The footnotes here aren't quite as in-depth but still worth mentioning since it adds to an already wonderful book.
I'm positive someone somewhere has described this as "Lord of the Flies meets Project Runway." Like some of her other books, though, Bray sets up gonzo premises in order to talk about pretty significant social issues.