The ones I use are from Wal-Mart for about 90 cents each; Costco is a bit higher. When it comes to your storage approach I can tell you what probably any other organization freak will tell you . . . There will always be something that doesn't fit the model. I find the shoe boxes ideal for things like glue/epoxy, jig parts, sharpening supplies, dust collection and edge guide accessories for routers and ROS, string and twine, tape and velcro, small scraps of exotics, light bulbs for machine lamps and so on. I will say that at the price, it pays to by extra (more extra than you think you'll need) so you will not get stuck with odd ball dimensions if you need a few more in 6 months.
The next size up in my chosen storage scheme is a 12.9 quart size from Costco. They do not show in their website but, in SoCal they are sold as Costco item #877572 . . . "Buckle Up Storage Set" and they come in a pack of 6. If you are already at Costco getting these I would just get the shoe boxes there too. The difference probably won't pay for your gas to Wal Mart ;-)
Once you get beyond this size I stick with drawers or shelves. 12 gallon storage bins are too large for daily use (although I use this size in the shed). they become too heavy or awkward for routine storage of quick-access stuff. I found I was doing things another way rather than fight the 12- 15 gallon bin size down off the shelf to get to what I knew was in there. Sounds dumb I know, but, it turned out to be true. This led me to the smaller bins.
So . . . .
Small storage:
I now have "Plano" compartment boxes for small parts (screws, hinges, knobs, nuts/bolts, washers, bumper feet). The Plano versions vanished from their lineup but, the Harbor Freight version, while not as resilient, have worked for about a year so far without the expected failures so, I would not hesitate to go there.
Medium storage:
the plastic shoe boxes from Wal Mart.
Larger storage:
The 12.9 quart Costco bins.
Big stuff:
Drawers, shelves or out to the shed ;-)