Is the latest version of PT as good as RS? I can't use Japanese with RS and I was able to with PT so was sorta hoping I'd be fine JBing again but this time with PT.
The only advantage of pwnagetool now is to install cydia applications into your custom firmware. Once you restore with that firmware you'll already be jailbroken. However the team hasn't updated pwnagetool (or warned people its a bug laden version) with the bug fixes that redsnow has received. So if you use pwnagetool you'll have to rejailbreak with redsnow to fix the bugs.
There are programs like aptbackup that claim to do this, I've never had success with them. I download the .deb files as cydia is installing them. You have to get them before exiting cydia or they disappear.