If you wish to prevent certain open (or minimized apps) such as Explorer.exe or Control Panel from automatically opening when you restart, navigate to HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Policies\Explorer. If the right hand pane doesn't have an entry for NoSaveSettings that is type REG_BINARY, add it.
Now, change value to hexadecimal 1 (right hand pane will look like 01 00 00 00) Close all applications (or you will get a scary message) and reboot.

Contrary to the Resource Kit documentation, this entry will not prevent you from placing new shortcuts on your desktop but it will prevent you from permanently repositioning desktop shortcuts and from adjusting the size and/or position of the Taskbar.