For my long cables, I do the electrician's wrap like this. I would post step-by-step instructions here, but it's easier to see than describe.
For my short cord, I do the "figure 8" wrap like this, like many people do for their headphones. Once they are wrapped, I put them in a small Ziploc bag. You can pick up a ton of these for cheap at a hobby store like hobby lobby or Michael's. These are usually in the craft storage or photograph storage section of the store. I think I bought something like 200 for 5 bucks.
All of these are stored in Rubbermade bins, by category. It really depends on how many cables you have, but I found this to be the best storage method. If you have less, I would suggest a duffel bag (it's portable!). Putting the cables and bits and pieces in the ziploc bags keeps them from getting tangled together.
Also, if you have trouble remembering what a cable is (or what it's for), you can always write it on a 4x6 notecard and shove it in the bag with the cable (I usually do part numbers, etc) to help keep everything sorted out.
Edit: Here are the storage boxes I was talking about from Hobby Lobby. They go on sale for 3/6$ occasionally, so you can just watch the circular ads. And here are the bags, also from Hobby Lobby. They come in different sizes, but they also go on sale for 200/3$. So for about 15 bucks, you can store cables and wires to your heart's content.
I keep mine categorized by Power (transformers and line cables)/AV (composite, component, and audio cables)/USB(micro, mini, a/b)/Odds and ends