Lots of good ideas on here. I'm a recent 4R owner (09 SR5 4WD) and wish there was more storage in these rigs - my Subaru Outback has more nooks to store things than this does. Currently, I'm using a zippered tool bag in the back to store larger items like fire extinguisher, road triangle, folding shovel, etc. It has small rubber feet on it, so it doesn't slide around too much. I've got a large first aid kit, emergency blanket/tarp in one side compartment; ice scraper & squeegee in another; cargo net, leather gloves & hitch pin in one of the wheel well compartments; misc survival gear (knife, matches, whistle, compass) in the other wheel well compartment; mag light rides in the driver's door pocket.
One comment on fire extinguishers - I carry a 2.5lb ABC extinguisher in my rig and recently had to use it to put out a car fire. It's amazing how quickly these get depleted. It was a small fire & I barely managed to get it put out. If you need to use one of these, you better have a good plan on where you're going to spray it.