Well, I intend to create "category" folders. For example, I have a folder called "System Tools" and have programs like "NIS 2005", "CCleaner", etc... listed in that folder. If I didn't do this, then I wouldn't be able to see all my programs listed (and my screen resolution is set to 1024x768).
Just do what I do, and you will also find it more easier to find a program you are looking for as well.
Please remember that SOME programs will want you to reinstall them if you do this, like NIS2005, so I just copy and paste the folder into the System Tools folder and hide the orginal so that NIS2005 doesn't want to be reinstalled.