I did try to find a good cohesive and cataloged system, but in the end I just ended up going with folders and descriptive filenames.

For instance, my music resides at "Music/Artist/Year - Album/Track# - Tracktitle.Filetype", with appropriate additions to the Tracktitle to signify bonus tracks, remixes, live tracks and featured artists.

I've adapted pretty much the same system for all of my other documents. It's a bit old-school, but it works.