my wife just got an iphone 3GS. we both have apple IDs, but her iTunes on her iPhone shows my username
Are you using the same user on your MacBook? If so, you're probably using the same iTunes too, which probably is set to your Apple ID. To use a different ID, you need to switch accounts every time you sync the iPhones. To sign out, choose "Store" > "Sign out" in the iTunes menu bar.

Thankfully, this whole hassle will be over when iOS 5 is released.