Another thing I have on Pinterest. (Yes, it's an addiction. lol.)
Or you could make your own dividers such as these. Same concept just tweaked. This way you might be able to get more Kongs stacked in a container than if sitting Kongs in cups.

Tutorial for above concept can be found here with the materials:
http://sharonscraps.blogspot.com/2012/07/how-to-make-your-own-organizing-system.html