JSPA Program Manager is an application for Windows Mobile 6.x (including 6.5.3) which allows one to easily manage your programs(shortcut links) in start menu. It allows you to Navigate, Move, Copy, Rename, Delete, Create New Folder, and install EXE files on an easy steps.
The software solves the annoying problem in Windows Mobile 6.5.3 of not being able to take shortcuts in folders to the root folder.
The software has recently been updated to version 3.2, which makes the application more finger-friendly and easier to use.
Read more about the free application in this XDA-Developers thread here.
Thanks Thomas for the tip.