I teach the kids to check the top pockets any time they're absent and then to ask me about make-up work. Kids remind me to (let them) hand back papers when some are in the organizer because I am notoriously bad about remembering to pass back what I've graded.
Not pictured are the bins where students turn in their work to me. Those aren't as interesting. They're simply stacked plastic file trays labeled with the class period. Simple, and they work!
How do you organize paperwork for your students?