full-disclosure - Verifying patches on MS servers

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From: FederatedInformationSecurity at federatedinv.com (Federated Information Security)
Subject: Verifying patches on MS servers

I've got a server that broke and had to be patched by uninstalling and
reinstalling a bunch of software, including various patches and maybe
even a service pack.  What's my best way to scan the server to make sure
no outdated .dlls were laid down or restored?  If I'm not mistaken, most
microsoft tools check the registry, which might not be accurate in this
case.  My options right now are ISS internet scanner, nessus, MBSA et
al, which is best?