How to make full back up of iPhone?
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.