I use 'Satco'-brand takeaway food boxes, which I buy in the hundreds.
Benefits:
Stackable.
Cheap.
Flexible. (so depending on the project/phase, the appropriate boxes get moved into a place where they're handy).
Self-sorting. (regularly-used boxes tend to be higher-up, so generally starting at the top and working down is an effective search method).
I store my breadboard wires in a breadboard. That way I can easily pick the right size according to the number of holes it covers.
My resistors and ceramic capacitors live in a folder full of pockets. I think it was designed for collecting baseball cards or something like that.
For tidy early prototyping, I made these several of these Uno/breadboard setups. The Uno is secured inside a plastic case, screwed to the wood (in this case sawed up from a donor empty wine case). Foam feet on the bottom help make it stable. It sure beats the uno and breadboard wobbling around all over the place, and can be put away like this without anything working loose.
