If you have the space, keep EVERYTHING... throw nothing away ever. I've been in the military 15yrs... I keep all boxes with all factory foam inserts or whatever for everything. I'm not specifically talking about gun boxes... but EVERYTHING. All computer, stereo, kitchen stuff, tools, TV's, all of it. Makes packing/moving every 2-3 years a piece of cake.
As for gun boxes specifically... it might add a little snap to a prospective buyer to know the previous owner kept and transferred the original box. It makes it easy to ship if you ever sell out of state, etc... Keep'em.