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One has to distinguish between long-term storage formats, and "terminal" (ie reading) formats. Personally I've standardised on MobiPocket as my reading format, but I use HTML or RTF as a long-term storage format. I don't know what I'll be reading my eBooks on in 10 years time, but I'm confident that whatever format it uses I'll be able to convert these storage formats to it.
I have a folder for each author, within that a folder for each book, and within that all the files associated with the book, both reading formats and storage formats.
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