I'm also planning the same project for my TJ, but I haven't settled on the requirements for it yet so I don't have a design.
You may want to think about how much you are willing to spend, since that will partly determine the materials you end up with. Because of my personal preferences, I wouldn't build anything for the jeep out of wood, no matter what it is. But, I'd definitely not make a cargo box of wood, and especially not for that location, which frequently gets wet in my experience.
Start with your requirements, such as--do you want some space under the box to store windows, etc? Would you like to be able to open the box from the top, and do you need to open it from the back? Does it need a drawer at all? How easily & quickly will you need to pull it out and replace the seat, if at all?
I'd like to have a separate, shallow lower drawer just for tools, with a larger upper drawer for camping gear. I'd like enough space forward of the box to allow a fair amount of recline on the seats, and/or to slip in a couple of 5 gal water cans. The top of the box needs to accomodate a removeable cargo tray for lightweight stuff such as sleeping bags, tent, etc.
Rigid makes a job site chest (model 2032) that I think will fit perfectly into the back end of a TJ. I see it as a starting point, at least, for a weatherproof, tamper-proof box. It's all steel, though, and so it would add a lot of dead weight. Aluminum would be nice.
Unless (and maybe even if) the box is 100% weatherproof, it's going to collect sand, water, leaves and all sorts of other crap, and will be a major PITA to clean out without some clever design.
I'd like to collect every idea anyone has come up with--especially for the short wheelbase jeep. This is an area that really needs some improvement.