xiaobenben

You can transfer your iphone apps back to iTune, but make sure your iTune doesn't have a newer version of that app. For example, you can delete the whatapps from iTunes then when you connect your iphone to iTunes, you can transfer your apps back to iTunes. Just right on your iphone in the iTunes, you will see that transfer menu.

For your JB apps, you can download an app from cydia and backup your JB apps.