It is mentioned on the Panic site, but it took me ages to find it.
You can add bookmarks or tags to a file that will appear on Coda’s code navigator. Most of the time it’s as simple as an !
CSS: /* !bookmark */ HTML: <!-- !bookmark --> Javascript: /* !bookmark */ or // !bookmark PHP: /* !bookmark */ or // !bookmark
You can of course replace the word bookmark with anything you like.
For a full list:
http://www.panic.com/coda/developer/quicktip/5.php