Over the years I have developed a specific way to store empties, but a lot will depend on how many supers and how much storage space you have. Another issue is pests. Mice and wax moths can be especially hard on stored equipment.
I keep empty bee boxes—with or without drawn comb–in stacks in an enclosed shed. I crisscross the boxes so that each box is at a 90-degree angle to the one below it. This allows the free flow of light and air throughout the stack. I have been told that wax moths do not like light, so a stack with lots of light inside is a good thing. I should mention that my shed (which is really my garden shed) has both windows and skylights. I know this seems like prime real estate for bee boxes, but I don’t use the space much in the winter anyway.
However, it is not a perfect system. Mice don’t seem to mind the light and one year I had mice make nests right in the drawn combs. They made creative use of chicken feathers, wood chips, peat moss, and straw they found in the area, and they munched on the combs that contained honey and pollen. So now I stack the boxes and place mouse traps on all four sides of each column and a few inside the stack on the floor. It’s worked so far.
Beekeepers who must treat their empties for wax moths often stack the supers in line with each other so no light and air can enter. Inside these closed off stacks they place insecticide to kill the wax moths. So again, it depends on your situation. I don’t use pesticides and I’ve managed to keep wax moths at bay by always freezing my honey combs after harvest and by stacking the empties as I’ve described.
The “open stacking” method also inhibits mold growth. One year I stored a few supers that had honey and pollen in them and, in order to keep mice away, I closed up the stack. By spring, the combs smelled moldy and disgusting. Since that time, whenever I have frames with honey or pollen, I give them to an overwintering colony. The bees manage to discourage mice, moths, and mold better than I can, so I let them.
I’ve seen people just stack their supers outside, but around here rain is a problem as well as lots of wildlife—including mammals, birds, and all types of invertebrates (bugs and slugs)—so I keep them inside.