Girl Genius is written in [ProWiki], a next-generation hybrid between a wiki and an object-oriented DB that I've been working on for a number of years now. ProWiki itself is effectively a prototype for the real implementation, [Querki], which I'll be starting serious work on in late 2007. That will be a very serious open-source project, so if you're a hardcore programmer looking to work on something seriously cool, drop me a note.
So many of the pages in this wiki aren't the usual unstructured text pages that a "normal" wiki has. Instead, they're complex data objects, with a lot of different properties, and the various "list" pages are actually queries into the database.
Major base classes and their templates: