I have mine set up or stacked on-end. They are on a rubber-backed carpeted floor. I feel that, due to the physical nature of the cylindrical structures involved, the best way is to stack drums is on-end because any load force placed on them when they are stacked is uniform and directed to the strongest aspect of the shape. Also, the "spring" or "piston" nature of the drumhead gives some shock absorbing to the stack.
A kind of "cradle" shelf (as pictured) would work fine, too. It just isn't as practical for my collection because I don't have that many snare drums. I have mostly drum sets.
As far as leaving them set up, I find it to be preferable....because that way, I play them! In some ways, I feel like I want to maintain my collection as best as I can, but, at the same time, I still enjoy playing the drums more than maintaining them. I mean, I'm mature enough that I won't throw them off the stage at the end of my 15-minute extended drum solo....like I used to dream I would do....but I also don't keep them hermetically sealed inside a pyramid, either.