I have a couple inexpensive and simple things that I've done in my FJ's rear cargo area. Not sure how unique they are, but after reading this thread, I haven't seen any of them yet.
Basic Tear-Away (Hook & Loop) First Aid Kit Pouch (Pouch by Condor, IIRC) Attached to Center D-Ring
Get Home Bag Secured by an ITC Grimloc
Fiskars Axe Stored along the Driver's Side with QuickFist Clamps
We all know that the stock cargo net doesn't work with the stock sub-woofer, right? Well, with two 18" pieces of paracord tied into loops and two NiteIze S-Biners, the net works just fine, thank you.
Edit: The storage box (barely visible behind the net) came from Home Depot ($8.98) as did the nifty black bungee cords ($8.89 for four of them) that secure it. The box holds recovery gear and cold weather gear (in season).