I stash a lot in the various cubbies and under the rear seats. The rest I have in a cheap, zip-up auto-emergency kit I got as a gift one year. It was full of cheap, crappy stuff which I threw away and replaced with better stuff.
You should also investigate tool bags, not boxes. I use them for my tools at home and you can fit far more in a bag than in a box, and it's easier to get at and easier to carry.
I use the same collapsible containers as CoKen has in his photos. I can fold them down out of the way if I don't need them. Currently I have one folded and stacked ontop is one with my emergency, towing gear in it.
Cardboard boxes, a taller one like what a ream of paper comes in and a lower shorter one like two shoe boxes in size. This way if they're in the way and I have something big to put in the 4Runner, I can dump it without thinking twice.