I use a wooden toolbox from an art store, a couple of round cookie tins (the Danish butter cookies you get at CVS) and the bench. And I also store my rattlecans on a shelf adjacent to the bench. My oils, my little square bottles of Testor's enamels, and some Model Master jars are in the tool box, Tamiya jars in the one cookie tin, and more Model Master and other, similar-sized jars in the other cookie tin. Craft store acrylics are on the bench.
I originally organized with an eye to portability, that is, that I would want to throw everying in a box and carry it to a show or a meeting. But since that happens infrequently, I'm thinking about adding a paint rack to my bench; I'm tired of having to dive into the box and the tins, and shuffle them around on the bench.
This reminds me of a couple of similar threads we had at Agape Models in the past few years. Here is a link to a discussion of the same topic:
http://agapemodels.com/forums/index.php?topic=992.0
And this thread is a discussion of making a paint rack:
http://agapemodels.com/forums/index.php?topic=3729.0
I have in mind something like that wooden rack, or possibly something like the rack that Scott/Yellowbird built out of angle stock and peg board, that you see in his photo (5th post in). Unfortunately, his link to his blog on building the rack is dead, so you can't see the SBS on building it.
I'd still like to have something portable, and I picture a clamshell box that opens to stand on a bench, but with a handle that allows it to close and be carried. I know that there are also tackleboxes and toolboxes that also allow storage and porting.
Hope this all contributes to the topic, prosit!
Brad