I've been trying to find the best software options to get started and they are both getting easier. But I don't think you can beat this new software called MakerCase by Jon Hollander. You just put in the dimensions and it creates the box for you. Then you can add round or square holes. On top of that you can add text to be etched on top of the panels. When your done it outputs a .svg file for direct import into a Laser Cutter.
I'm just getting started with this software to see how well it works and I have a place near my workshop that does laser cutting for a low price, so this may be my first step towards making my own boxes for my electronic projects.