Important information for iOS 9 and 10 users!
CopyTrans Apps now allows you to backup iPhone apps to PC
To back up iPhone apps, check out this tutorial instead: How to backup iPhone apps
The manual way explained below is no longer required.
Transfer applications and purchased music back to iTunes
Connect your iPod Touch, iPad or iPhone.
WARNING: To avoid “Automatic synchronization" of your iDevice by iTunes click and keep the Shift and Ctrl keys pressed while you open iTunes. Please refer to this FAQ article.
Wait for iTunes to detect it.
Select the device from the devices section.
Right click on the device name once it appears on the left-hand side pane and select “Transfer Purchases” and wait for the sync to complete.
NOTE: if you don’t see the side-pane, pres ALT then once the menu options appear on top select “View” and then select Show Sidebar”
That’s it you are done!