Within iTunes click on 'iTunes' in the Menu Bar, and go to 'Preferences'
Then click on the 'Store' tab, and uncheck 'Apps'
i take you wanted to stop iTunes from automatically downloading Apps your purchased/downloaded from your iPhone, but i could be wrong, you mentioned syncing, so I'm a bit confused as to exactly what you meant, but hopefully i'm correct.
Wirelessly posted (Mozilla/5.0 (iPhone; CPU iPhone OS 5_0 like Mac OS X) AppleWebKit/534.46 (KHTML, like Gecko) Version/5.1 Mobile/9A334 Safari/7534.48.3)
What I do, is go ahead and click "remove from device" and then click "apply" then immediately unplug the device befor it actually starts to sync. The setting will stick and the next time you connect it will not remove the apps.
Wirelessly posted (Mozilla/5.0 (iPhone; CPU iPhone OS 5_0 like Mac OS X) AppleWebKit/534.46 (KHTML, like Gecko) Version/5.1 Mobile/9A334 Safari/7534.48.3)
What I do, is go ahead and click "remove from device" and then click "apply" then immediately unplug the device befor it actually starts to sync. The setting will stick and the next time you connect it will not remove the apps.