I have mine mostly categorized by function: Fiction, Non-Fiction, Manuals, Newspapers, Manga, Personal Docs etc., and a separate FBReader folder since those documents can't really be used by the standard DR1000 software anyway. Then, if several if the books are part of the same set/series I may have a subfolder for it.
That's good enough for now, I don't have too many books, and it limits the number of click-throughs. Also keep in mind that the list/details view allows one to see many more documents on the same page (plus added info)
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