the emergence of small market!
If you want to get local vegetables and products, you can get them at the "cooperatives" if you are not in any large city center and if you have a car. You can also shop at small markets: the posh (and expensive) one is located in Aoyama, close to the UN University. There is another one in Yurakucho, and, a new one, in Kachidoki. There must be a lot more but these are the one I know.
It is a bit more expensive than your local supermarket but they are fresh, tasty and sold by the farmer directly. Besides markets is also a gathering place for small restaurants-in-a-van: curry, pizza, coffee and waffles, makunouchi bento, ...
If the weather is fine, try to find some quite place in a park and enjoy your bento! It is just great!