I organize everything in a semi-coherent fashion, as far as files and directories go. Navigation is by way of HTML menus that I code myself - they're simple, but effective. My past archives have followed a pretty specific format, including the following sections:
The immediate purpose of the archive is to provide a point of reference for me and my coursemates to use, both for drafting our dissertations over the summer and for future projects in which we may be involved once we rejoin the work force. Additionally, I'd like to streamline it for possible use as a marketable project at some point in the foreseeable future.
Once I complete the archive, I'll post an update outlining the various sections, and I may include some of the links for everyone's situational awareness. I expect the project to be well worth the effort, even if I wind up being the only one to use it.