The much awaited Pwnage tool 3.1.3 is finally ready for download. Thanks Dev Team, now we can successfully jailbreak iPhone 3GS for  3.1.
Download Pwnage Tool 3.1.3 from Rapidshare mirror here if you have a Mac. No Pwnage tool exists for Windows platforms.
Custom 3.1 firmware links below for the following iPhone models :

iPhone 2G 3.1 (Original iPhone)
iPhone 3G 3.1
iPhone 3GS 3.1