Most programs that show in the system tray will have a configuration panel with a check box somewhere in the options to enable/disable it showing there when it runs.
There is a list somewhere in the registry or an *.ini file that shows/hides items in the Add/Remove Panel. Usually it is tweaked to show programs that are installed but not usually shown there. So presumably one would need to modify that list. If I can find it I will post back, but a bit of searching for Add/Remove plus a few keywords might come up trumps.