We use a crate to store all of our current school books so that they are all contained in one place.  I chose a crate instead of a box because I can put hanging folders in the crate to separate each subject.  Binders and large books are placed in the back of the crate without a hanging folder.  With this system each book or subject is readily accessible without much searching.  When our next child is ready for formal school, we will use another crate for that student.  Here is a picture of my crate:

I use a plastic caddy to store school supplies such as pencils, pens, crayons, scissors, glue, money, ruler, etc.  See picture below: