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My system is pretty simple: one large "ebooks" folder, and then author folders inside ("King, Stephen", "Pratchett, Terry" etc). Inside these author folders folders are book folders, since I have every book in several formats: the original LIT, the exploded HTML, the HTML0 from Book Deisnger, a LRF for the Sony, pictures for the cover page and anything else related to that book.
I don't use calibre or any other software for book organization because I don't want to get tied down to a particular application.
Folders are portable, simple and get the job done very well. Of course, when you want to transfer something to the Reader via any app, you just load it from it's folder.
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