I do not know how this happened, but suspect that you upgraded to IOS5 and that caused all the apps to be enabled in the app tab.
Without phone connected open iTunes, Edit > Preferences > Devices (tab) and put a check by "prevent iPhones, ... from syncing automatically".
Then connect your phone to computer, and select your device, go to app tab and uncheck the apps that you do not want to be on the phone.
You can run a sync then. Also you can go back to preferences and uncheck the "Prevent ..." if you are satisfied, but as you add apps to your phone, you may want to leave it checked and control the sync manually as described.