Finally got around to hacking my Junksorter script, and came up with a solution for files located on a users desktop. Fairly ugly hack, but it works. Also, it looks like in Gnome 2.5, Nautilus is going to switch from using scripts to a plugin system. This should be pretty cool, since the plugins will be written in a lower level language, there should be a decent performance boost.
Modified Junksorter Script