As promised, here is the update, including the editor, and compatibility with a bunch more programs.
It now supports Windows Explorer, 7-zip, WinRAR, FileZilla, ACDSee Classic, XnView, xplorer^2, Directory Opus, MS Office 2007 dialogs, and console windows.
Included is the alias "fafedit", which will allow you to easily edit your favorite folders list.
Additionally, I've updated the FarrFolders.exe so that it handles command-line arguments correctly. AHK has a problem with command line arguments that end in a slash, so I've gone with a windows api method that handles those correctly, if double quoted. It will now handle the quoting for you.
Anyway, enjoy, and let me know if there are any problems.