This page will cover several popular methods of making project boxes with the help of the Laser Cutter. Most of these methods are designed to cope with the constraints of brittle Acrylic, but many of the methods can used accross different materials that the Laser Cutter supports.
The Fingers Method
That picture pretty much sums up the finger method. You make little slots and little grooves that connect to each other. The only downside is that you will likely need a little adhesive to keep the sides together since the grooves are not exactly tight.
DON'T make your own! Use the great website that does it for you: http://boxmaker.rahulbotics.com/
Just type in the information and hit "design it" button. Open the resulting PDF in Adobe Illustrator and delete and superflous lines then print away!