I suppose the biggest problem is the way bundled games come in some instances. For example, SMAS+SMW was a bundle only pack in, with no box. Then there is Tetris with the Game Boy or Sonic the Hedgehog, which was bundled with Genesis core systems, also with no boxes, but it was also released in retail, or like the MGS4 PS3 bundle or the RE5 360 bundle, which included MGS4/RE5 with their full retail packaging. And then there is Wii Sports and Super Mario, which come with their manuals and a cardboard sleeve.
I've been pulling my hair out, trying to organize it all. And trust me, there isn't enough there that I can afford to be pulling on it. ha