I've been looking and looking for sturdy, inexpensive, yet visible ink pad storage. I am currently using photo (or also known as media)boxes for my ink storage. I can place the box on it's side, lengthwise, and have three stacks of ink pads. I currently have at least 24 ink pads in one box on my table top. I have the lid sitting across the top of the box holding my markers. You just have to be sure you don't pull out more than one ink pad at a time, but they stack up just fine.
Hope this helped out someone! ~ Frances "Phoenix Chica"