This from the Microsoft Knowledge Base:

How to Prevent a Program from Being Displayed in the Most Frequently Used Programs List?

WARNING: If you use Registry Editor incorrectly, you may cause serious problems that may require you to reinstall your operating system. Microsoft cannot guarantee that you can solve problems that result from using Registry Editor incorrectly. Use Registry Editor at your own risk.

1. Start Registry Editor (Regedit.exe).

2. Add an empty string value named NoStartPage to the following registry key, where Program name.exe is the name of the executable file that is used to start the program:
HKEY_CLASSES_ROOT\Applications\Program name.exe

3. Quit Registry Editor, and then restart the computer