My bench is my tool caddy:
In all seriousness, though, I really just suck at putting things away. But when I do, it's VERY organized.
From left to right...
Cheap Target 4-drawer cart thingy (seriously about $20): One drawer for airbrush stuff. One for pigments, a few washes, oil tubes, etc. One for metal and plastic and spares. And another as an emergency drop for laundering new kits into the stash or hiding any gifts for the wife. It sucks and it wobbles when you open a drawer, but it gets the job done.
Paint rack: Two crappy shelves my wife bought somewhere. Linens and Things maybe? Been in our garage for five years, so I stole them. Used empty Diet Dr. Pepper cans and PVC tees as supports. Holds all my Tamiya, Gunze and Alclad paint beautifully.
Chest of many small drawers thing (cheap, from Lowe's): Holds Model Master enamels organized by color (blues, browns, metallics, etc). Use the empty bins for spare PE, or as temporary holding bins for WIPs
Main bench, bench-level - three gray storage dealies from Target I think - one holds glues and adhesives. Another is primers, putty, silly putty, white-tac and such. And the last is decals, foam applicators, and so forth.
To the right of that and off-frame, I have a little two-drawer desk organizer thing. Top drawer is knifes and cutting implements. Bottom is tweezers and pliers. A little flip-up storage area on the top holds extra blades.
Going vertical, I've installed some elfa shelving that we had leftover from consolidating rooms as kids arrived. Going up one level, bins for Vallejo paints (which are just too tall to fit in that red chest thing). Above that, more bins. One is dedicated to sanding sticks and files. Another to things like my circle cutter, digital caliper, etc. And the last to masking materials.
I've found, for me at least, organizing around task works really well as far as finding things, with a few of those super-common tools easy-to-hand.