The iPhone Dev Team have released PwnageTool 3.1.4 and thus the iPhone 3GS is now supported out of the box which basically means if your iPhone 3GS is upgraded to 3.1.x in iTunes you can still use PwnageTool to work its magic reports softpedia.
Apparently, owners of iPhone 3G or iPhone 3GS who rely on Untralsn0w to unlock for use with unsupported carriers will lose the ability to unlock employing the tool and thus should perform the iPhone 3.1.2 firmware update via iTunes.
However, if your iPhone 3G or iPhone 3GS uses ultrasn0w for mobile service you should only update with a .ispw which is made for PwnageTool 3.1.4 states the iPhone Dev Team.
Users of the iPhone 3GS and iPhone 3G can employ PwnageTool and then restore with iTunes using the newly created .ispw.