I have a few cib nes games (DK, Legendary wings, maniac mansion, tmnt, super C and my sealed DW1) but otherwise its cart only. I hate Nintendo cardboard boxes. I cant believe they used them all the way up to the Gamecube. I really like the boxes that have the sleeve encased in plastic (the Genesis style) that someone on ebay sells. Id love to have my entire NES collection in them but that would be way too much money on a bit of flash.
As far as the rest of my collection, my PS1 and my Dragon warrior/quest stuff I want 100% complete otherwise its just game.