Customizing Doxygen Output
Doxygen provides for a handful of ways to customize the output. If you want full control over all of the Doxygen objects, you can have Doxygen output XML and then write your own output generator to do anything you want. The drawback of doing this is that it requires a substantial effort. It is much easier to simply customize the Doxygen HTML output.
Doxygen allows you to customize the HTML output by modifying the master HTML header, footer, and stylesheet. The following command will generate the default Doxygen HTML files.
doxygen -w html header.html footer.html customdoxygen.css
The Stratify documentation is built using this technique.
You can grab the code from github.