A classic problem in creating a design for a site like this is that the main navigation menu cannot really be centralized. Some sections, like "Undergraduate" and "Graduate", are controlled centrally, and should appear on every single page that uses the CS Department template.
Other parts of the site, however, may not fit into the menu structure. As an obvious example, the site administration tools certainly shouldn't be linked within the site's main menu, but while viewing administrative pages those links need to be there.
Within the site administration section, any faculty member can add
custom menus for specific URLs. Here you can see a simple menu that
appears when viewing pages in /~bfenster/openhouse/.