There has been a few cases where I've ended up doing a V2P migration (which is extremely rare, but usually for something that, by policy, has to be on its own hardware, or that I create the VM and get the app in place and tested, then image it to a machine's bare metal for production use via WIM or another mechanism.) I'm sure these will leave the VMWare client files running, but not doing anything, similar to how a Hyper-V to VMWare migration leaves the Hyper-V files present.
In fact, if one turns on Hyper-V in Windows 8 and newer, it might register as a VM to malware, even though it essentially is just a single instance.
Ideally, depending on environment, I've found that separating the system from programs under Windows is tough. Reinstall the system, and most programs will need to be reinstalled due to Registry entries missing. Some programs can allow this (mainly MMOs, oddly enough -- WoW, Rift, EQ, and EQ2 can be split off and run on a Windows instance without reinstallation), but most won't. So, for Windows, keeping one's data separate is more of a focus than splitting the application from the OS.
OS X has a similar issue (mainly because /Applications can't really be moved to a separate partition , but I could be wrong.) However, it is easy to move /Users to another partition.
Other operating systems, a system, application, and data separation makes sense. In AIX, this is something you are supposed to do, so you can have multiple rootvgs available . Linux, it is good as well, since you can split /opt off and reinstall without affecting applications.
: In high security installs of AIX, no process has root. UID 0 can be configured to be just a schmuck user. To update these where no process has the ability to install software, the rootvg needs to be rebooted, another instance of AIX loaded that will do the OS updates to the secure one, then the machine (or LPAR) gets booted back to the secure OS root.
: Wish Apple would bite the bullet and add ZFS into OS X as a root filesystem (and not via FUSE.) This way, it really doesn't matter where what data is physically located where, other than the code for booting.