itunes seems to sync my wife's iphone with all of MY apps

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.

I am assuming that you have one account on the machine with iTunes. @deiga is correct. It will sync all apps that are selected regardless of who "owns" them.

A way around this that may work is separate logins on the machine. On either Mac or Windows, you just create a separate user account and then login as you and 'your' instance of iTunes. I have not tried this on Windows but it works fine on a mac.