In building a site powered by Jekyll and hosted by GitHub, I wanted the ability to highlight the current page's tab in the bar. I also wanted the bar to support second-level items (i.e. a dropdown), which proved somewhat tricky. This is the solution I arrived at after a few hours of fiddling around.
The contents of the navigation bar are contained in a data file located at _data/navigation.yml. This makes it accessible via the site-wide Liquid element {{ site.data.navigation}}. You can see the file for the formatting I used.