You can use reStart to reorder your icons.
I use Total Commander to put the links into folders that make sense for me. If you want to do this from the desktop, it will work but requires a bit of effort. Use ActiveSync and browse to the root of the phone. On the desktop, you need to change the Folder and Serch Options to allow you to see Hidden files and Operating System files. (In Vista, Organize>Folder and Search Options>View).
Once you do that, simply browse to the phones Windows\Start Menu\Programs and you can see your folder structure. From there you can move things around and add or delete folders to your liking. Once that is done, use reStart to put the icons in the order you want.
Hope this helps.
Here is a link for reStart
http://forum.xda-developers.com/showthread.php?t=481379
Doug M.