The Bodleian library in Oxford is one of the largest in the world, and they have a very simple way of organizing books: They are numbered as they come in, go onto a shelf in that order, and an entries are made in a database saying where to find each book.

I use more or less this same approach: Everything goes into a stack, and when I need something I just do an interpolation search through the pile using the date of the document as a key.