Always keep them in the box they came in. Stacked in a hall closet or special game and puzzle cabinet or closet area is good also. Stacking them neatly keeps them easy to find too.
Make the system easy for the people who actually use it: visible categories, reachable storage and a clear place for each item to return. For younger children, a picture label can work better than a written one.
My final check is practical: can you find what you need quickly, put it back just as easily, and see when the space is getting full? If not, simplify the categories or move the storage closer to where you use it. An organizing system should make life easier, not become another chore.
Mr. Organized's Answer