Some more examples to throw into the ring:
HTML5, doing crazy things with how we move through “pages” and arrange information: eephusleague.com/magazine/

E-lit, with its history of making web design choices that emphasize affect and narrative (sometimes at the cost of credibility and legibility, but sometimes at the gain of powerful emotional impact)

Dynamic webcomics such as Homestuck (mspaintadventures.com/), which does a bunch of non-traditionally-comic stuff such as transmedia (e.g. music albums, analog book meta-remediations of the born-digital comic) and interactive gameplay. A very slow start reading-wise, but it does really pay off (it’s even on my Ph.D. exams list!)

If we did end up talking about the practical side of making “weird monographs” like the ones people are suggesting, I’d be interested in creating a list of actual small tools people would like to see–things you could install on WordPress, Omeka, or Drupal that would make your next piece closer to the tools it sounds like this session would imagine. I’ve been thinking about developing plugins like this for my dissertation, and I’d love to help other people realize some of their publication needs.