I don't know if you're looking for something simply for display (i.e. to keep the dust off) or if the fit needs to be more snug to actually protect the box from bumping around when being moved, but the variations in box sizes may prove to be a problem if you're looking for a one-stop solution for the latter case.
I just did a quick google search and turned up this site that has boxes of just about every length x width x depth imaginable. If the variation in box sizes proves to be problematic in finding a standard one-size-fits-all solution, this may be an option, though at first glance they do not come cheap.
That was just the first one that popped up, so if you can settle on a standard size, you might be able to find a supplier with more economical, standard options. Also consider other collectibles that are about the same size as the box you are trying to accommodate for which a standard display case might already exist (off the top of my head, I'm not sure, but maybe Nascar cars or something similar?)