How to make full back up of iPhone? With iTunes popupmenu



I have just restored my iPhone from a backup from March 2012. However all my apps made with Xcode was sadly not restored.

How can I back up everything? 

Besides Xcode apps, which other things does iTunes backup not backup?
You don't get a backup of developer builds that are not ad-hoc builds (and thus synchronized with iTunes).

You also don't get backups of music, movies, podcasts. If you set the iPhone to be manually managed by you, you have to add all media back yourself. (Except ringtones and your photos)
I don't know, whether iTunes will resynchronize your media if you don't manually manage it.