This is my method as well. A few weeks ago I took out a book from a shelf because and then couldn't put it back even though it was on that shelf a few minutes ago.
I like the first-in-last-out sort method. I mentally order the shelves from top-to-bottom, left-to-right, like one long linear list of books. As I pick books off the shelf and read them, I always put them back at the top left of the book case, and shift the rest to the right and down as needed. Then I see my favorite or recently read books in one location, and books I've never even touched at the bottom.