I'm starting to accumulate more charms as I cut down larger pieces. Currently they're in a ziplock bag, but I think ultimately I'll use an Art Bin. To keep them from falling, I'll wrap a stack the way I wrap my strips and strings--loosely with a selvedge tied around with a bow.
You can determine if you'd prefer to organize them into stacks by color or theme, and how large a stack works for you. I'll probably go with 1" inch stacks sorted into neutrals, lights and darks, and keep I Spy squares their own stack.