It would seem that if files are being maintained in some sort of repository, then perhaps an antivirus filter should be applied to them at the point of entry. If a site allows anonymous users (or just not-too-bright ones) to upload files, then this could certainly become a problem. Check out ClamAV. It looks fairly easy to use, and has a MS counterpart. In fact, since it has a command-line interface, it might be a rather simple task to implement.
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