I've been looking for those plastic containers that are slanted in front and open. Not sure if I'm describing it correctly but basically they are in their own container but you don't have to open them up - you can just reach in and grab them. I've seen small ones in michaels and a lot of grarage stores - for little screws and bolts. I think those would be perfect for all my different shaped cutters if I could find ones a little bigger. I know they're out there I just can't find them.
Have you tried Home Depot or Lowe's? I think I've seen them there with the garage storage items. I'm not sure they would work as well as the boxes, though, because I think it would be hard to see what is in each bin.
I use the plastic shoebox system that others have mentioned. I took the time a couple of months ago to type a list of all my cutters in alphabetical order so I could refer to it to see which box a particular cutter is in. I printed it in a small font so I could fit it on one page, and I actually carry it in my purse because I kept buying cutters that I already had!