These are a godsend: http://www.thewarehouse.co.nz/red/catal ... KU=1778852
Well, when they're on special.
Anything that can fit in those, is stored in those. My collection is mostly PC based, but those are fantastic for software, accessories, 8 bit style home machines etc
For me I have 4 main storage locations, inside, garage, storage unit and an area under our house (for us it's walk in and dry/warm - no computers there though).
Inside the house I keep a small selection of my favourites / most used. In the garage I keep enough bits for testing or any projects I might decide to do or any project I'm currently working on. Everything I'm unlikely to need or want to use in the next few weeks stays in the storage unit. When I want another machine to use from storage, I use a 'take one bring one' system to prevent too many systems from ending up back in the house. I recently had a cut down of machines in the house because we had to make one room in to a nursery.
Another trick I use for storage is for parts, but would also apply to many early home computers as well, and that's using old clothes drawers. Guests need not know if it's full of socks or Commodores, and it doubles as a bench/work area. For CRTs or awkward shaped machines I don't have a good solution yet - mostly I use "under desk" space and shelves.