Why not use the search function on the reader itself? It works well. Then organize them into collections for easier sorting. No rooting or other programs required.
It takes time to do it at first if you have 100's of books on the device but then just do it for each book you add. Overall though it doesn't take that long. I've had to do it twice with 300 - 400 books because of the stupid sync thing deleting my books. I was mad but I got it done relatively quickly.