There should be more novels with footnotes, I think. Especially in YA novels. Why? Because footnotes allows an author to have a witty aside that doesn't mess up the flow of the main story. And there's not enough witty asides in this world.
If you haven't read a YA novel with footnotes, why not give one of these a try?
John Green: An Abundance of Katherines (who, coincidentally, has written about the appeal of footnotes in novels)
Jonathan Stroud: Bartimaeus books (The Amulet of Samarkand, The Golem's Eye, Ptolemy's Gate, and The Ring of Solomon)
Daniel Ehrenhaft: Drawing a Blank
E. Lockhart: Ruby Oliver books (The Boyfriend List, The Boy Book, The Treasure Map of Boys and Real Live Boyfriends)
Michele Jaffe: Bad Kitty
Any ones that I missed? Drop me a comment!