My personal preference is a lidded rack system. I prefer to move the cage to a working area and then open it rather than have it open while I'm sliding the box out. It just seems safer this way.

One of the best things that I've found is just get you some 3/4" square steel tubing and weld up a frame and use plywood or MDF of whatever board of your choice for the shelving. This way you can build one from the ground up to fit the dimensions of whatever box you choose to use as a cage.