Yeah, one file per format is in my opinion definitely the biggest obstacle if one is thinking about using Calibre to organize other things.
.zip is an option and I use it here and there if needed but a whole library with zipped files does not seem convenient.
Adding files as separate records and grouping them as a series (or using another column for that) is another option - but it requires a complete change of habits and makes it more difficult to simply browse the library (sooo many records). On the other hand, one could use e.g. some custom search or a virtual library to display only one file per item while simply browsing the collection.
Another option could be to store the data outside of the Calibre library and link to them in book details - but this would be quite difficult to maintain as one would have to manually change the link if any changes in the data folder were introduced. It also makes it more difficult to copy a library, and from what I've seen, Calibre uses full file path for links, not a relative one (or is there any option for a relative one). It would also be nice to have simply links to folders, not files (that's not an option either, or is it?).
That's why I've created this thread - hopefully, there are people who've come up with solutions they're really satisfied with, and they could share their insights

. Or there are users who've found other software solutions for other kinds of data - maybe not as flexible and customizable as Calibre, but good enough.
Waiting for inspirations
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EDIT: Just to clarify, I agree with you, theducks, that 1 file per format is good for e-books. It's just not optimal for storing other kinds of data (which is perfectly fine, it's not what Calibre has been created for, after all). This is why I'm looking for powerful workarounds or alternatives - I'm basically spoiled and that's, by all means, Calibre's fault ;P.