I bought some plastic coupon cases that have tabs insdie from the Target dollar store. I labeled one case just for squares, one for circles, another one for ovals, etc. Have six different cases that cost me a total of six dollars.
Then I found business card size magnet calling cards that I didn't need. (My daughter had lots left over from her wedding Same the Date magnets. Had others from pizza places, the library, etc.) I cut those up and mounted them on index cards. The nesties fit perfectly on the magnets on the index card. Each square set is stored in its own little tab section so I can find the size I need very quickly and easily.
Keeping them separated into squares, circle, ovals, etc, makes it fast and easy to just grab the square storage case when I need a square.
Very cheap and easy to maintain. Not to mention, to store.