I am working on documenting my website code into both a funtional design document and adding JavaDoc style comments for use with PHPDocumenter. While working on the database side of it with fresh coffee in hand I am reminded of the choices that went into the taxonomy of the db for the site itself. Basically using a portal idea and a public/private as the grouping for the navigation and child pages. After that it all kind of fell into place.
It all starts on a good foundation of organized content.