I'm not sure what the OP is getting at. If a back-up drive is failing, and it has installed programs on it, what's the point of wanting to uninstall those programs? Recover created files, yes. But uninstall the progs? Are you saying you haven't got those program install disks and somehow need to mirror the disk to the new one?
If you do install a new disk exactly as the old 150Gb, the same drive letter should be assigned, the same shortcuts should work, and the registry shouldn't care a hoot.
If you're NOT wanting those progs again, then, yes, some sort of registry cleaner, or if you're feeling brave (where's Keef?) do it by hand.