The only programs that could be simply copied over from one drive to another are those self contained in one folder only where the installer creates a desktop shortcut and no entries in the system registry plus other hidden folders and installation logs that Windows itself creates.
With multiple versions of Windows as well as multiple drives any downloads with self installers are simply backed up on removable media, a separate partition, or even a totally separate drive. Once one version is reinstalled fresh on the same or other drive all programs are reinstalled as well.
The files and settings transfer wizard in XP and Vista's backup feature are the tools provied by Microsoft for seeing things restored when simply wiping the first drive or seeing that version of Windows go onto a replacement drive like when upgrading to a larger model. That's how it works. And simply using a cloning software doesn't provide any guarnateed results either. A new mbr and other things like hardware profiling have to be considered.