The shop I go to has gallon ziplock bags of scraps and they are $10 each. They are usually strips and big sample pieces from manufacturers. Good, but not cheap.
I tried putting my 2" squares away in my 2" square box, and unless every single one was perfectly stacked on the one below it, they didn't fit neatly into the compartments. So I ended up using the box for my 1.5" squares, the smallest size I keep. That worked better-- more 'elbow' room for my squares! Wish I could find one with a little bit bigger compartments.