I haven't done this myself yet as everything I use is just off the shelf items. But, if I were to do it...
I'd use two layers of waffle foam (the black/grey stuff if you can get it) for the top (lid) layer and the very bottom layer. Then I'd use some closed cell foam (black) for the middle layer, and cut the shapes to fit my guns.
But that's just me. Some one here made a nice pulse rifle crate and used foam with a camo material cover over the foam. It looked pretty nice as well.
In fact, you might even be able to use the camo cloth over some standard white chair/bed mat foam. You'd start with... say 1/4" thick piece of plywood as a base. Making sure it fits inside of your crate/gun box.
You'd then use some sort of foam material for the bottom layer, probably a 1.5" chair seat foam. Then cut your gun shapes out of 4" thick white bed/bench seat foam. Then lay your cloth over the 4" thick foam, pressing it into every corner in your cutouts and using a staple gun, staple the foam down into the plywood base, through the 1.5" bottom cusion.
Sounds complex, but it really Isn't. Just time consuming planning everything out. I did something similar while making an "ejection seat" for an airsoft game. The wooden frame of the seat was pretty rough but the foam seat itself was pretty sweet.
Russ
"Time has little to do with infinity and jelly doughnuts."