I have built a standard sweater box rack with 1/2" plywood sides, melamine shelves, and no back... just a simple cleat to stop the box from sliding through the back. You can also tape on foil-covered styrene insulation for an insulative back and to save weight.
I'll be posting a general rack building thread for someone else later today. You can read more about spacers there. But to answer your specific question, with leopard geckos the space is not that important. I would probably go with a 3/16" gap between the top of the box and the shelf above it. I have kept leopard geckos in racks before and I did not have a problem with crickets escaping from this sized gap.
Regardless of what you use, I do recommend finding a box that does not have the invidual raised "feet" on the bottom. They work much better in lidless racks, especially for geckos that typicaly have heavier substrates.
Here's the picture of that rack. In this photo I was no longer using it to house animals. Instead it became a drawer system for my herp supplies and a colony of mealworms. You can see it has a width wise inserstion. In other words, one full sized box can slide in width wise OR two half sized boxes can slide in length wise.
This design is always lighter AND is much more versatile. Highly recommend it unless space is an issue.
