I keep most of my stuff in my '05 TJ in ammo cans - one of the really big ones (think it's a 20MM one) and two of the "fat .50" cans. I also keep a mechanic's bag in the back with ratchet straps, bungees and such in it. For carrying larger items I have a hitch-mount cargo rack that I put on when I need it but don't usually have on the Jeep.

I keep a ton of tools and spare parts inside the Jeep, no-one ever messes with the stuff because it's all hidden in cans and a bag that are always covered in mud, grit, grease, and dirt so it looks like there's nothing worth stealing.

I swapped out the rear bench seat to a racing-style bucket seat to give me more room and mounted my Hi-Lift jack to the roll cage across the back pillars horizontally. Both my fire extinguishers are mounted to the roll cage right behind the front seats and there's a little storage under the rear bucket seat.