After just stacking all of my cybertron deluxes in a plastic container, the only thing I can really tell you to be careful of is translucent plastics, (obviously), (don't store longarm on crosswise), and soft rubber plastics, eg; the tailfins on thundercracker, mine bent a little. Otherwise, whatever.

I didn't ziplock bag my figures, the plastic bags can scratch, I only ziplock bagged instructions/accessories. Great way to get instructions flat without ironing them.