When are you guys going to figure out that tools aren't like seeds? If you plant them, they won't grow new tool trees. :D (That's what my old man used to tell me when I'd use his tools as a youngster and forget to put them back in the box.)
For me, the key to organization (when I take the time to get organized) is putting things together. Screwdrivers together, wrenches together, etc.
Do it in any order that makes sense to you. I agree with a lot of the guys who are putting the most frequently used tools at the top. Saves from constantly bending over.