How to tell iPod Sync not to include my iPhone apps?

Does anyone know when I sync my iPod and also to back it up to my computer, that it should not copy my iPhone apps to my iPod? Why does iTunes assume I want my iPhone apps copied to my iPod. It's actually my sons iPod and he certainly doesn't care about my apps.

I cancelled the sync and I think this is why I cant update my sons iPod to the latest iOS5.1

This is getting frustrating. I really don't understand why iTunes can't be simpler to use !

Thx