The iPhone Dev team has released the latest version of their iPhone Pwnage Tool 3.1.3.
Pwnage Tool 3.1.3 will let your upgrade your iPhone 3GS or iPod Touch 2G to iPhone firmware 3.1, but only if you are using a custom jailbreak on your iPhone 3GS with firmware 3.0 or 3.0.1.
The iPhone 3GS is now supported in PwnageTool 3.1.3, assuming the phone was pwned at 3.0 or 3.0.1 – PwnageTool does not support the 3GS out of the box. If your iPhone 3GS has 3.1 pre-installed and is not Pwned then there is no tested jailbreak solution at the moment.
If you have already upgraded to version 3.1, you wont be able to Jailbreak your iPhone with the Pwnage Tool 3.1.3, you will have to wait until the iPhone Dev team releases the next version.