For me the issue is more with games or DVDs (not to mention my comics) than books, having only couple dozen that are particularly mine.
I've always created rather elaborate ways to organize these by subject, genre, maker/publisher, how highly I personally value them, what I still haven't played/watched/read...
And with PC games there's the additional problem of some being old boxes of various sizes and most DVD cases.
Comics, while largest by volume and numbers, are the generally the easiest to organize, large part of them consisting of certain magazines.