[graemian]

I assume the side-by-side view is rendered from the raw file with comments inline? Is this using some kind of comment markup language?

Where can I find out more about cool ways to render comments like this?

[hey_lu]

It's generated using http://jashkenas.github.io/docco/. I think it's possible to use comments, but often it's "literate" source code, e.g. markup & code blocks.