I follow, in both our mechatronics lab and in my home work shop, the Adam Savage theory of first order of retrievability. Tool stack drawers are truly the death of hand tools. When working you can never find what you need and have to move other stuff to get to it. It's nice to see everything that you have and nothing is hidden. The main part of the system is that the things you use the most are the easiest to access. Some stuff can still go in drawers, but you can easily do away with a bunch of tool stacks. I recommend you check out some of Adam's tool organization techniques on
http://www.tested.com.