Universal media cases are sold by mediashelving.com and hold NES, Atari, Nintendo 64, Genesis and Super Nintendo games nicely. Not only that but they have a clear outer sleeve similar to that of DVD boxes for artwork. Their is a website called The Cover Project (http://www.thecoverproject.net) that is dedicated to producing high quality artwork of the original boxes that fit these cases (and DVD cases for disc based systems like 3DO and Sega CD) perfectly.
Its a nice solution for me, because even though Id like to have all my games complete in their original boxes, this route is much cheaper (in the long run) and protects my games from dust and damage. Plus the cases are much sturdier and look awesome lined up on a shelf.
Just thought I'd share this for anybody who's looking for a nice neat way to display their collections.
http://www.mediashelving.com for the cases
http://www.thecoverproject.net for the artwork