Bill wants to know how to back up his programs when he backs up his data. Leo says don't. It's problematic and rather difficult to do that, plus it'll take up a lot of space. What Leo recommends is to image the drive and use that as a backup. He can then blast it back onto the hard drive whenever he needs. Here are a few imaging programs to try:
Leo uses SuperDuper for the mac. The nice thing about SuperDuper, he can create a bootable image.