The jailbreak for iOS 6.1 just arrived, but Apple had to quickly introduce two emergency patches to the OS to fix Exchange support and a lock screen privacy bug. Thankfully, you can still jailbreak the updates, but if you're already running iOS 6.1 you might not want to hunt down your apps and tweaks again. Here's how to make it a little easier on yourself.
Backup (and Restore) Your Tweaks with Free Software
We've talked about backing up your jailbreak apps manually, as well as with AptBackup (which actually just backs up a list of your apps, not the apps themselves), and PkgBackup (which does, but costs $10). Those all work fine, but we prefer OpenBackup because it's free, easy to use, and backs up everything you need. Here's how to use it:
Download OpenBackup in Cydia.
Open the app and select "backup." This backs up your iOS device to either iCloud (if it's enabled) or directly in iTunes. It also stores a local copy if you want to be doubly sure about the backup (you can find it at private/var/mobile/Library/Preferences/OpenBackupFiles and then save it to your computer's hard drive with software like iFunBox).
Open up iTunes, and then download and install the newest version of iOS.
Head into Cydia and redownload OpenBackUp.
Select the "restore" option in OpenBackUp, and let it do its thing.
Wait for your iOS device to respring, and you should be done.
When OpenBackup is complete, you device should restore with all the tweaks and Cydia apps you downloaded originally. In the end, you have a lot of options for backing up Cydia apps, but the reason we like OpenBackup is because it provides that extra failsafe of both a copy on your machine and iCloud. It's also essentially the same process as PkgBackup, but it's free. If you want to pick and choose which apps and tweaks to backup, PkgBackup is the way to go, but if you want to do it in one quick swoop, OpenBackup was the most reliable for us.
Take the Opportunity to Get Rid of the Apps You Don't Really Need
An automatic backup and restore option is fantastic, but personally I actually prefer the process of manually downloading everything again so I can clean out the clutter of too many tweaks. I've also had mixed luck with all three of the backup solutions listed above, so I tend to provide a failsafe anyway. Figuring out what's slowing down your jailbroken phone is kind of a pain, but when you manually reinstall everything you can really track down where a problem might be.
Generally, I just pop into Cydia and write down the apps and tweaks I want to reinstall. If that sounds too tedious, Appinfo is a simple little app that'll export a text list of all your installed apps and sends it to you as an email. Then, when you're updated and jailbroken again, you can just go through the list and reinstall. It's tedious, but at least it keeps things clean.