I've seen a number of ways that people have organized their bento box collection, which can get pretty challenging as the collection grows. Some people have the fortune to have enough cupboard space in their kitchen to dedicate soley to bento impliments. I've also seen people use freestanding cupboards, book cases, or whatever spare space in their dwelling that they could scrounge.
Though my apartment is relatively well endowed with closet space, most of it isn't conducive to holding small plastic boxes. Thus, I've had to improvise.
Voila! Plastic bin of bento boxes!
This holds all of my boxes, bags, egg and rice molds, along with a few random drink bottles. Stacking things vertically helps keep the mess contained, since I don't have to worry about a box avalanche if I'm grabbing a box on the bottom. Usually, the top is closed, so the boxes stay nice and clean. The only down side is that finding something specific can take a little work if it is stored on the bottom.
Does anyone else have any interesting bento storage methods?