i havent tested this yet to see if it will work this way(and wont until redsn0w is made to jailbreak 3.1, i wont even update my itouch g2 from os3.0.0 till it happens)but i have "apt backup". what it does is save code somehow in a way that when i back up, everything i got that is for jailbreak(things i've ssh's, things from cydia and icy) then when i restore, my backup gets applied(putting all my itunes app store apps back and such) then jailbreak, then get "apt backup" again and hit "restore" and it reads the file that it hid in the files backed up, and somehow i get all my jailbreak stuff back. when redsn0w is compat. w/ 3.1, i will try it. if it doesnt work, ill say so, but i hope it works. no big deal if not tho. i just have to get a few apps and themes and ssh some crap

also, this app wont backup the settings in ur jailbroken apps, nor their locations on ur springboard, but it will put all u have installed via cydia/icy again. most of my jailbroken apps dont need settings anyway, and i have them all the last pages anyway
i have provided the link to the "more info" page(w/ a screennshot and explaination of the app) that u get when u go to more info for the app in cydia. it can be seen on ur computer's webbrowser
AptBackup