I do something similar. It's currently implemented with IIS/SqlServer, but should work in *nix land as well.

The scripts use the name of the virtual host as an index to a database table which specifies per-site options, including style sheet names, logo graphics, etc. This, combined with the use of HTML::Template, allows customization of look-and-feel, as well as a few functional differences in the various sites, while maintaining a single codebase.

Of course, you have to have a database available...