Unfortunately this is largely a Windows-ism. Sure there will always be exceptions and the fault is equally that of the developers, but the disease that is the Windows registry means this will pretty much never be possible for Windoze in its current architectural state unless applications stick to being self-contained in a read-only app directory and keep their settings and temp files in the user profile. There is generally no need to splatter crap all over the OS, but most do it because they're too ignorant to write a clean application. I notice that apps ported from other operating systems which use configuration files (very efficiently) as opposed to the registry to store their settings have no problem being shifted from pillar to post.
I've done what you're suggesting, on hundreds of Linux servers, to take advantage of new virtualisation technology. Without touching the installed apps, without touching the guest virtual machines.... The occasional reconfigure of the app to work with new libraries is about all that's required, but again only if they're not static binaries.