In the TED Talk embedded below Sunni Brown, author of Gamestorming: A Playbook for Innovators, Rulebreakers, and Changemakers, presents the case for encouraging rather than discouraging doodling in the classroom and in the boardroom. Her talk might give you some new ideas about why your students are doodling in your classroom.
Warning: Ms. Brown does use one analogy in her talk that is not appropriate for the classroom.
If you’re interested in learning more about using sketches and doodles as thinking exercises, I also recommend Dan Roam’s The Back of the Napkin.