I'm going to phrase this hypothetically, but it's based on a real scenario:
Suppose you have a collection of software from the late 1980s/early 1990s. The floppy disks have been imaged (and you still have the original media) and a virus check run across the entire collection turns up about a dozen infected files out of a total of ~15,000 files.
Suppose further that you've run some additional analysis and determined that the infected files are
Not false positives - that is, the virus check results are accurate
Not duplicates of uninfected files.
Integral parts of the collection
Now suppose you want to preserve and provide access to those files, including the viruses - with clear warnings about their content, of course. What are some techniques you could use to do so? Build a second environment for infected files? Wrap the files up in a container like WARC, as suggested in a previous question about infected files?  Other thoughts?