If you don’t want a program to display in the "Most Frequently Used Programs" List change the following registry information:

Hive:	HKEY_CLASSES_ROOT
Key:	Applications\<Program name.exe> (where Program name.exe is the name of the application that you do not want to be displayed in the Most Frequently Used Programs List.
Name:	NoStartPage
Type:	REG_SZ (String)
Value:	(do not enter any value, leave it empty)

That’s it. Reboot your computer.