So long as you don't delete the iTunes folder that should be created when you first install iTunes then your apps will be safe. Subsequent re-installs will not override that folder (usually created in your Home or My Documents folder).
If you wish to make a copy of that folder for your own back-up needs then you can simply either copy the entire contents (which will also include any music, music video or film purchases/rentals you may have either purchased or copied into your iTunes library) or drill down inside the folder to find the Mobile Applications folder.
On my Mac and previous PC whenever I updated iTunes my library remained intact. I can only presume if you choose to uninstall iTunes you will be asked if you wish to keep your library or not.
Hope that helps