I just use searches and alphabetical ordering and looking around the locus of a search hit. This is actually better than a bookshelf would be, because you can sort on more than one thing and resort in a fraction of a second rather than having to spend several days reshuffling everything. Combine that with full text search across all books and honestly I hardly even use categories any more: they're even redundant for grouping series, unless the series is written by multiple authors.
Everyone talking about "better organization" seems to think that the Kindle is competing against a full-blown relational database or something. It's not. It's competing against physical bookshelves, and there, there is no contest, except that your eyes can scan physical bookshelves quite fast because the field of view is much bigger than a Kindle screen. (But it still sometimes takes me ten minutes to find a book on my bookshelves, even though they're sorted by author. It never takes me remotely that long on the Kindle.)
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