Organizing class folders by color coding each class has been very effective. For example, 1st period student file folders may be all green folders, 2nd period student file folders may be all orange folders, 3rd period student file folders may be all pink folders, etc.
This systems has worked very well for me. If I need to pull a certain class or subject set, I already know what color to refer to. If I need a select student, I know the class or subject that the the student is in so I then know what color set to refer to.