They stay in the box so when resale time comes.. people who want a bag to keep in the box can have them.
This. Plus what longtallkarl said.
Everything except the lens, lens caps and hood stays in the original box, which goes into a storage tote in the attic. I have a dedicated photo equipment shelf in one of the hall closets. I leave whatever lens was last used on the body, and store it on that shelf with the battery (-ies) removed; the other lenses, speedlites, accessories, etc. are all within ready reach. One shelf up are my seven camera bags (I almost have as many bags as bodies and lenses), providing a variety of sizes and well-padded configurations, so no additional lens protection is needed.