when the new pwnage tool came out i ssh'd into the prefs folder (i think /var/mobile/Library/Preferences) then copied all of the prefs. upon jailbreak and reinstalling of apps, i put these prefs back. most of what i wanted got saved.
also, using applink, i went into the actual application folders and copied out the Library and Documents folders and replaced them as well.
of note, the file permissions may need to be repaired after putting them back, but i don't have the details for that step right now. if you don't correct file permissions, then things will NOT work correctly. that step took a while to figure out (ie, why SMS, phone, etc were crashing).