It's an overflow "failsafe" system that was apparently adapted from the Herbie system (which I never could understand the concept) and developed by BeanAnimal. The theory behind it is that you run your overflow drain just slightly slower than your return flow, causing a little bit of overflow to go down the second drain - which creates a completely silent overflow. It also acts as an emergency drain in case your primary drain gets clogged. The third drain tube is an emergency backup in case both your primary and secondary drains get clogged. It is designed to be noisy in order to alert you of a serious problem while preventing a flood. You can check it out here:
http://beananimal.com/projects/silent-and-fail-safe-aquarium-overflow-system.aspx
If you noticed the pictures of my overflow box, it has three drain tubes, which is the method described by BeanAnimal (see link, above). the secondary drain and the emergency drain are going into those lines.