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While I backup my ebooks in various ways, cloud, hdds, you really can't do much better than calibre, so I also recommend it for basic ebook file storage.
Beyond that, I compliment if with a database of my own design, plus all the benefits of using an XLS spreadsheet, which also includes physical books, and that I started many years before calibre existed.
An XLS spreadsheet if created right, can get around the various limits of calibre, when it comes to sorting and searching, and assigning things like multiple series or sub-series that a book may belong to. Of course, calibre does lend itself to tweaking, if you are savvy enough. I generally personally prefer to leave it standard, just as storage and adding/removing ebooks from devices, and editing names & titles where necessary. Right tool for the right job as they say.
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