What is the proper way to store tires to prevent cracking?
A lot of this is guesswork on my part. 

Entire bike: I would deflate the tires, keep them on rims if possible, and hang the bike up. Putting weight on the tires when they're deflated is probably bad for the tires -- and for the rims. 

Rims with tires: I would follow zigdon's answer and hang up the rims and deflated tires. 

Bare tires without rims: I'd store the tires on their sides, not stacked too high. Perhaps putting them in something like a pizza box, or between pieces of cardboard, would help avoid the tires crushing each other. 

In general: I would also flex the tires every so often, to stop them from getting brittle. Also, ozone is bad for tires, so I'd not store them near anything that generates ozone (furnaces or electric motors), and I'd store the tires away from extreme heat or cold.