I don't own them myself, nor do I display my toybiz stuff in dioramas around my room.
However, if I did have a set up with some dioramas, I'd probably take all the crates and set them up warehouse style, with Spiderman jumping over a few and Doc Ock knocking a bunch over. Basically, do up the scene from the 90's TAS.
Not doing dioramas, I'd probably throw them out.
Another option, should you want to hang on to them, is display the figures on top or in front of the boxes. It would take up a little more space, but not by much. I usually keep my boxes for statues, busts, and Medicoms, and I do that a lot.
You can get pretty creative with it, really makes quite the nice display. IE, take them and put them in a Pyramid-Staircase like set up, then place a row of figs in front on the bottom, then one each on top of the available spots.
The last option which I've never liked, is box them up. Throw them in a plastic box and toss it in your basement or garage or closet or something. A box full of boxes. Waste of space, IMO.
Oh, another good one- presents for your lady friends- tell them it's a jewerly box.