Magic Folder is a cool ahk script that puts a magic folder on the desktop that allows all folders and files to be organized in a 'hidden folder' (which is not really hidden but located at a user-specified location).
I don't know how to describe it other than to say that it I have been using it for a few months and find it to be very helpful.
http://www.autohotke.../Magic%20Folder.html 
