What do you do with all that stuff you acquire when you get a new computer? You're overrun with disks, manuals, cords, instruction sheets, warranties, adapters and packaging, all of which is different shapes and sizes. Years ago, I had a client who carefully slipped each disk into a plastic sleeve in a binder. A second binder with still more sleeves held the paper documentation.
The main problem with that kind of storage is that there's a good chance you'll never look at or need any of those things again. So it makes no sense to waste time organizing them. My advice is to use one of my favorite organizing tools: the versatile zip lock bag.
Just take all that stuff you want to keep (you may need it after all, so I don't advise pitching it) and throw it into a bag. Lots of stuff? Use the gallon size. Use two. I like the kind that uses a zipper pull to close it; for me they're much easier to open and close.
Besides being incredibly easy to do, this method lets you keep everything in one place. Otherwise, you'll either spend a lot of time labelling cords and adapters and other miscellaneous parts, or you won't have any idea what they are when you encounter them next year.
I keep my bags in my computer gear drawer upright, like file folders. If the manual has a title on its spine, position it in the bag so that it shows through the side or bottom, then file the bag so that the spine faces up, giving you an instant label. Even without a label, it will be easier to find a particular bag when you can thumb through them. If they're in a horizontal pile, you'll have to take them all out to find what you need.
Colored cords from Jim 5's photostream