Q: Since the release of the iTunes App Store, I’ve accumulated a number of applications for my iPod touch that I don’t necessarily want to keep around, at least not in their current versions. Is there any way I can remove these from iTunes to unclutter my application listing but still get them back should I want them later? I know I can prevent them from syncing to my iPod by unchecking them in the Applications tab, but I just want them out of the way in general, but don’t want to have to purchase them again if I decide later on that I want them back. Any ideas?
– Jeremy

A: There are a couple of different ways you can go about handling this. Obviously if you don’t need to keep the applications around at all then you can simply delete them from iTunes as you would with any other item: Right-click on the application in the iTunes application listings, and choose “Delete” from the context menu.
As with other types of iTunes content, when you delete an application, you will normally be prompted first to confirm that you actually want to remove the application from iTunes, and will then be asked what you want to do with the actual application file:
If you want to keep the application around for later, simply choose “Keep File” and the application package itself will remain in your “Mobile Applications” folder along with your other App Store purchases.
This folder is located under your iTunes library folder—generally your Music/iTunes on a Mac, or your My Music\iTunes on Windows. You can also go directly to this folder by right-clicking on any application from within iTunes, and choosing “Show in Finder” (Mac) or “Show in Windows Explorer” (Windows).

You may also notice when visiting this folder that multiple files may exist for a given application. This is because iTunes keeps earlier versions of an application on-hand whenever it is updated from the iTunes App Store. This is a useful feature in case an application update does not work as expected, but you may want to visit this folder every few months and clean out the older versions that you don’t need in order to conserve disk space.
Normally the most recently-dated copy is the latest version, but you can confirm which version of the application iTunes is actually referencing by right-clicking on an application in iTunes and choosing Get Info from the context menu:

If you’ve removed an application and later want to reinstall it, you can simply locate the application’s IPA file in the “Mobile Applications” folder and double-click on it or drag-and-drop it into your iTunes window. The application will be reimported into iTunes in the same way as a music or video file would, and will appear in your iTunes applications listing. Note that as with applications newly-downloaded from the App Store, any applications that you re-import manually will also be immediately selected for synchronization to any iPhone or iPod touch devices that are syncing to this library.
Lastly, keep in mind that at this point at least, iTunes does allow you to re-download any applications you have already purchased at no additional charge. Simply attempt to re-purchase the application, and instead of the usual confirmation asking if you want to buy the application, iTunes will let you know that you’ve already purchased this item and can re-download it again for free.