Most programs store their work files in My Documents, and it's a good idea to educate your users to store all their files in that folder. Many users however prefer to store their work directly on their desktop because it's "more accessible" that way i.e. one click instead of two. This can be a bad idea however, and here's why.
System Restore is a feature of XP that lets you return your computer to a previous "snapshot" in case something goes wrong and your system becomes unstable. Now if users store their files in My Documents and they have to restore their system to a previous state, that's OK--none of their files in My Documents will be deleted or changed in any way i.e. they won't lose their work by restoring their system to a previous restore point.
But if they store files directly on the desktop and then restore their system to a previous restore point, some of their files may get lost. In particular, executable files stored on the desktop will be deleted if you try restoring your system to a previous restore point. That includes exe, bat, cmd, and com files. Other files on the desktop that are deleted during a restore include hlp, inf, ini, vbs. msc and dozens more.
So train your users to store everything in My Documents if you let them use System Restore.