jashkenas has single-handedly redefined literate programming for me. I've always considered it somewhat useful, but never very practical until seeing his annotated sources.
ever since seeing Dox I have made a much larger effort to essentially create a reference for everything I write (in a perfect world this would be a given).
More examples:
Underscore: http://jashkenas.github.com/coffee-script/documentation/docs...
Backbone: http://documentcloud.github.com/backbone/docs/backbone.html
CoffeeScript: http://jashkenas.github.com/coffee-script/documentation/docs...
I believe they're all generated with Docco: http://jashkenas.github.com/docco/