By now, you have surely downloaded one or two (or more) applications that you no longer desire to keep. You don’t just want them off of your iPhone, you’d like them gone from your iTunes Library as well.
1. Open iTunes.
2. Go to your Library and select Applications.
3. Find the application you wish to remove and right-click (or ctrl-click) the icon.
4. Select Delete.
5. iTunes will ask if you are sure you want to remove the application from your library, click the Remove button.
6. You will then be asked whether you want to move the application to the Trash or keep it in the Mobile Applications folder, select either the Keep Files button or the Move to Trash button.
The selected application will be removed from your iTunes Library.