From LedHed's Wiki
Slipsteram SP2 into Windows 2003 Server R2
Extract the contents of both CD's then do the following:
WindowsServer2003-KB914961-SP2-x86-ENU.exe /integrate:C:\W2k3\disk1 WindowsServer2003-KB914961-SP2-x86-ENU.exe /integrate:C:\W2k3\disk2