The ones on the older shelves are by category, but when I have built more shelves, I have not taken them all off and re-organized them. I have shelves almost every where they will fit. After I read a book, if it will not fit on a shelf, it goes on a pile on a chair or something, until I have company, then I put them in a box and put it in the storage area.
I have a lot of family books too, the oldest are a KJV from 1841 and a Webster's from 1849.