I've found the best storage for the MiniDiscs are the wood boxes that cigars are sold from. If you go to most cigar stores with a MD to test with and some cash (they sell in Michigan at around $5.00 - $25.00 depending) you can probably find one of their used cigar boxes that'll fit your requirements. The regular MD fit well for me in the "avo No.5 TUBOS" boxes with a sliding lid, which I get for $5.00. I can fit 62 - 68 discs in one.
p.s. - I think a cigar box was used to store a data disc (MD?) in the beginning of the first Matrix film
