No doubt because of my perpetual struggles to remain organized, I believe we owe it to our students to teach organization skills. Long after they have left us and likely forgotten 90% of the particulars of our disciplinary subject matter, they will, hopefully, know how to organize their work materials.
I have seen teachers hand students a sheet detailing the specific notes and handouts they expected to find in their notebooks as well as how to organize these components. I have known some teachers to collect these heavy artifacts once or twice a semester. Well, that all seems like way too much work for the teacher with not enough responsibility falling to the student. Dana Huff, over at HuffEnglish, though, offers the best approach to notebook checks I’ve come across, thus far: creating short (10 questions based on notes/handouts/writing responses from a specific class date) notebook quizzes and allowing students to organize their notebooks using a system that works. It seems to have the added benefit of making students responsible for catching up on missed work and notes.
I would try to arrange a notebook quiz once a month.