The App Store is loaded with extra applications for the iPhone and iPod touch, and Apple did a great job of making it easy to download and install all of those programs. The problem is that not every app you download is something you want to keep, and deleting something from your handheld doesn’t necessarily mean it will go away when you sync.

Instead of starting with your iPhone or iPod touch to delete unwanted applications, start with iTunes and do this:

• Select the Applications Library
• Control-click or Right-click on an application you want to delete.

Control-click to delete an application.

• Choose Delete from the pop-up menu.
• Click Remove when iTunes asks if you really want to remove the application from your Library.

iTunes gives you a chance to change your mind.

• iTunes will ask what you want to do with the deleted application. Click Move to Trash if you want to remove the application from your hard drive, or click Keep Files if you want to keep the application, but remove it from your iTunes Library.

Send apps to the Trash to remove them from your hard drive.

Now connect your iPhone or iPod touch to your computer. iTunes will display an alert because your handheld and iTunes Application Library no longer match. To make sure your deleted application stays that way, click Don’t Transfer. Clicking Transfer will copy the just-deleted application from your handheld back into your iTunes Application Library undoing the delete process you just went through.

Don’t Transfer keeps iTunes from copying deleted apps from your handheld.

Deleting App Store downloads you no longer want isn’t quite as straight forward a process as it could be, but it is easy to follow once you figure it out. Maybe Apple will surprise us with an iTunes update that makes it simpler to delete those unwanted apps.