itunes seems to sync my wife's iphone with  all of MY apps my wife just got an iphone and she did her first sync and its syncing all of my applications (i have an ipod touch).  Is there anyway to have us sync to a separate list of apps? 

if i delete these apps off my wife's iphone, are they going to be removed from itunes (and then my ipod next time i sync ?? )
Anything removed from an iOS device is not removed form iTunes.
Secondly, iTunes sync's all apps that are specified to sync, no matter whose App it is.
iTunes determines the owner to be the Apple ID, which downloaded the App.

Here is an example o the app sync window:


Here you can choose the apps to sync. And remember it will upload apps belonging to either of you, but it won't change ownership of them.