I just have a folder for each genre and make the ebook filenames '<Author Surname> - <Title>.pdf'. This way the books are arranged by author name and there aren't too many folders to dig through.
I would much prefer a FBReader style system which enables ebooks to be given multiple tags, but most of my books are PDFs which FBReader doesn't support.
I'm currently writing a desktop program which manages my ebook collection like iTunes manages music (so whenever you plug your digital reader in, your library is automatically synchronised). I might incorporate Grimulan's neat idea of using shortcuts to link to ebooks from multiple folders.
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