I LOVE the way I store my Nesties ...
I use DVD clear plastic sleeves (bought from Target in a pack of 25 ... I'm on my second pack ... shhhh) ... they are the same height and width as the DVD cases, but SO much thinner!
I cut cardboard to fit into the sleeve and then glue a magnetic backing to it ... each Nesties set gets its own sleeve. I then cut the thin cardboard label from the Nesties package to fit in the sleeve, so I know what's in each one easily AND how many dies are in the set
All the sleeves fit easily upright in a small plastic open top tote with a handle (what you might keep make-up in) ... I organize them by type (ovals, circles, labels, flowers, motifs, and so on) and can easily access what I need.
The whole thing takes up about 6x8 inches on my desk and I can find what I need in a few seconds (and it cost very little)