I've just upgraded to iTunes 5 and iOS 5 and after the process completed, my apps are missing from my device. I can still see them in iTunes under Library/Apps folder, how do I push them to the device? (I've tried sync already but it did nothing.)
When you connect your iPad/iPhone you choose your device in left column under the Devices section, then got the Apps tab and select the Apps you want to sync (Screenshot in german but looks the same in english):
Afterwards select "Synchronize" at the bottom right to update your iDevice.