Well I had this problem too very recently (last week :-D).
I had a "free" room almost completely packed (80%) with all my empty box-sets and some other emtpy carboard boxes.
Since I don't have room for my Steelbooks anymore I thought If I have this room emtpy I can put 3 billy shelves here and use this for my steels.
Here's a pic of the carboard boxes:
and here of the emtpy room: I had some carpet left and so it looks nicer.
So I throw away a bunch of carboard boxes away that I thought aren't very special or if I ever sell them I wouldn't get much with or without the original box anyway.
The Head Editions where the biggest and I think I only kept the Alien carboardbox to store inside other box-sets^^ and the Head Edition will be
the last thing I would ever sell so I through them away because they just take too much space.
Next week when I have the two other billy shelves I might have to throw away some more away but I don't regret it.
If you don't have the intention to sell why keep them and without them I have more room for new stuff
I mean of course if you sell them you will get more money with original box set just for the save shipping etc.. but I think it was the right decision.
But I thought about this a long time so I get it if you want to keep them. I mean I would advise to keep them if you have the free storage but now it feels really good that I can finally use this dead space again.
How it looks now