If it is XP/2003 machine you can initiate cmd.exe through AT command which will bring up cmd.exe under "System" account. you can run any application from that command windows will open it under system account.
AT time /interactive cmd.exe
On Vista onwards the interactive mode doesn't work so eventhough the application opens up it will not come on to the desktop. So simple method is run using psexec, a free tool available on sysinternals webpage. check for "PsTools".