I don't understand what you mean by that? You mean a method of removing/adding programs to the system try via normal dos commands? I don't think there is - unless they can be called directly by stopping or starting services.
== 4t Tray Minimiser== GUI Based
4t Tray Minimizer lets you running applications minimized as System Tray icons, which helps in adjusting free space on your taskbar. To minimize any application to the task bar, simply left click the minimize button as usual or press keyboard shortcut. You can configure 4t Tray Minimizer to automatically hide/restore specific applications by pressing specific keyboard shortcuts. http://www.4t-niagara.com/tray.html
== Trayconizer.exe == Command Line Based
Use this one to launch programs, then when you minimise, it drops it in the sys tray. http://www.whitsoftdev.com/trayconizer/
i.e.
Start > Run > c:\temp\trayconizer.exe "C:\program files\Internet Explorer\iexplore.exe"
- Or set the shortcut of any program to read like the above.