I tend to use a RAR file instead of a ZIP file as that does not conflict with Calibre's use of ZIP files for HTML documents.
I have also used .iso files where the relevant files come on a CD by just making an image of the CD and storing that in Calibre. If I later need to us the .iso file I can use a utility such as Daemon Tools to allow me to mount the image and get at the contained files.
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