The thing I get asked the most is how to update a jailbroken phone so that you don't lose the jailbreak apps, settings, configuration, layout, etc. So my first few posts here will cover that process, starting with backing up your Jailbreak apps.
There are three different methods you can use and I'll start with the first, easiest and cheapest: a Cydia app called AptBackup that has this logo:
Note, this is not the same as AppBackup, which can only backup stock apps, not JB apps.
Go to Cydia and install AptBackup. If you try to run it now it may bomb out so to fix it run Backgrounder (you have installed that, right?) and add an override for aptbackup and in that override turn OFF "Enable at Launch" as you can see to the right. With the most recent versions of IOS AptBackup seems to run smoothly right out of the box, er app store.
Click "Backup" which should only take a second or two and then you're back at the AptBackup screen. While you won't see anything what it has done is create three files in an area of your phone that gets backed up to iTunes when you sync. (Geeks keep reading, Others skip to the next paragraph). Those files are:
A list of your Cydia apps:
Cydia repos & details:
Your ssh configuration:
Sync to iTunes.
That's it. You now have a list, on your computer, of your Cydia apps, their configuration, the sources where you got them and some other stuff you probably don't care about.
Next, the easier, $8 way to backup your Cydia apps.