I would like to configure my servers to shutdown Windows via a script without actually turning the systems off.
Software for most UPSs will manage this. You configure the system to turn on after a shutdown, often after a certain percentage of battery charge is recovered. This means that if there is a second second power event, the system will have had time to fully power up and then power down again. I usually set this to 40% but it depends on the load.
PsShutdown is a command-line utility similar to the shutdown utility from the Windows 2000 Resource Kit, but with the ability to do much more. In addition to supporting the same options for shutting down or rebooting the local or a remote computer, PsShutdown can logoff the console user or lock the console (locking requires Windows 2000 or higher). PsShutdown requires no manual installation of client software.