I've got more old game cases + instruction manuals than I can count, but the only 2 console boxes that I've still got around are for my PS3 and my 3DS XL. As it is, aside from my handhelds, my PS3 is the only main console I have left, so it didn't make sense at the time to keep the boxes around too, especially if they were just taking up space. I know some people hold on to them for sentimental value or as collector's items, but I honestly wouldn't have the space to keep them around anyway, since I've got next to no storage at my new place.
I do wish that I still had some of my original Genesis boxes, though. I would've only been about 7 or 8 when it stopped working, but I'm not quite sure what ever became of it.