If an abnormal crash occurs and the game still appears to be stable afterwards, I would not be concerned about it. If the game started exhibiting stability issues, I would nuke (remove) the entire folder and do a fresh install.
What I do is make a copy of the hard stuff that does not change. I save off the head positions (*.hps) and stick stuff (*.jsm) to a CD, after I have it all configured. Then it is less painful to remove the game and reinstall it.
It is not enough to use the Windows remover. You need to remove the folders from the computer and then install a fresh copy.
I have not had to do a reinstall on mywork computer at all. It has been patched from V1.04 to the current version and is still stable. Patches do not make the game unstable, unless you get a corrupt patch (running Norton or any anti-xxx during the patch download/install can cause it). Actually, having Norton installed in Vista or Windows 7 could cause corruption as there is no way to stop it from doing what it does. All you can do is stop it from reporting what it does.