You want the system root for the desktop? I know %systemroot% is C:\Windows. I don't recall anything that would lead to the desktop...
You could try C:\Docume~1\%username%\Desktop\
That would get you to the desktop.
For example, if you have a batch file on the desktop that's called 'random.bat' then you could type in command prompt:
start C:\Docume~1\%username%\Desktop\random.bat