There were some reported bugs for users with the Mac OS X 10.5 and above with the PwnageTool and the iPhone developer team has resolved those with the latest PwnageTool 4.1.1 release. This release as stated is more of a bug fix for the Mac OS X Leopard users. Which means that you should only run this if you are on the stated Mac OS X 10.5.x version and ae prompted with Cydia errors.
There is one warning though, especially for those with iPhone, iPod Touch or the iPad and who have used the UltraSnow to unlock their devices. The problem will arise is when you let the iTunes restore your official IPSW. If the procedure somehow completes you can bid adieu to your unlock and worst still there will be no way of going back again. In case you accidently end up doing this unplug your iOS device before the updating firmware step starts.