If you haven't read "S" by JJ Abrams, you've got to! It's a publishing masterpiece! The actual book was made to look like an old library book which two graduate students pass back and forth writing in the margins trying to solve a mystery of the fictional author. There are codes, inserts, things stuck in the pages...the book even smells old with some pages with tear-stains. There is no one way to read it. I chose to only read the margins but even that has a system.
When my friends and I read it, half our discussion was "How did you read it?" which is really exciting to think about. Each reader approaches it differently. The multiple plot lines are great too (as would be expected from the creator of Lost) but I really enjoyed the actual physical book the most. A great example of meta-fiction as an emerging genre!