The concept of themes looks interesting. For anyone looking to see what a theme looks like, take a look at https://github.com/jashkenas/docco/tree/master/resources/par..., though it doesn't look like that is the same theme as the backbone docs.
https://github.com/jashkenas/docco/tree/master/resources/lin...
... just a template that gets fed the list of parsed and printed sections, and a bit of CSS. Nothing too fancy.