Granted, I download more apps as a tech writer than the typical iDevice user, but if you've had an iDevice for more than a few months, however, it's likely you have deleted many needless apps and free trials after trying them out. The problem is that if you delete an app from your iDevice, the app remains listed in iTunes. This is good if you might one day want to redownload it, but it creates a rather lengthy and unmanageable list when you go to sync your phone. In my case, I have more apps in the Sync Apps list in iTunes that are no longer installed (unchecked) than those that are, making it a chore to sort and manage the apps on my iPhone and iPad.
When viewing the apps on your iDevice in iTunes, you can check and uncheck apps from the Sync Apps list to add or remove them from your iDevice when you sync next. If there are apps listed that you know you'll never return to, you'll notice that there is no way to delete them from this list.
If you click Apps under the Library header in the left panel of iTunes, however, you'll be able to permanently delete apps, removing them entirely from iTunes. Highlight an app's icon or a group of icons by holding down Shift and hit the delete key (or select Edit > Delete from the top menu or right-click on an icon and selecting delete).
A window will pop up, asking you if you are sure you want to delete the selected apps. If you are certain of your intentions, click the Delete Apps button.
Next, to remove all files associated with the apps you selected for deletion, click Move to Trash on the next window.
Now, when you return to the apps pane in iTunes to sync your phone, you'll see that the apps you deleted are no longer listed. And if you deleted an app that is currently installed on your iDevice, it will be removed upon your next sync.