A few years ago I built a rack that clamps to the factory roll bar (such that it is) in the bakc of my TJ. It was high enough to slide the cooler, a milk crate and tool box underneath it (all the heavy stuff), and still have easy access to the light stuff on top. Cost was around $60 in materials, assuming you have access to a welding rig and cutting tools. Brad Kilby used to sell a similar rack, but his was a bit more refined, powder coated, etc., but ~$300-ish.
A side benefit to these kinds of racks is that with the top and doors off, it left a fairly secure storage spot in the back. The only access was through the door-hole, past the seats. Good enough to keep things secure while you run inside for a bite to eat, etc.
"Life is meant to be enjoyed, not endured" ~someone