What I've taken to doing is booting a rescue CD, creating a top-level "/old-system" directory, and moving all the top-level directories (including mount points etc) into it. That leaves me with a disk that is clean enough to do a fresh install on without needing a format, and when the install is done, all my old directories and files can be mv'd back into place as needed. Of course, I do backups *too* but I don't use a restore as part of an upgrade.
