I have a very small shop now, and some God-awful shops in my earlier years. I vowed when I got my own shop it would be my own shop. And I think that is where the battle for organization starts.
My woodworking shop is just that, for woodworking. If it does not relate to woodworking, it goes elsewhere. Like my snowmobile shed. That is where I work on my snowmobile. That means I have two sets of tools. Wrenches and sockets to fix my woodworking tools, and wrenches and sockets for my sled. It sounds expensive but its really not. If I need something special from my sled shed, I can walk over and get it, but for 95% of the stuff I need while woodworking, its right there, organized and quick to reach.
If you want to get organized you really need to go through your shop, take everything out that is not woodworking related, and make a place for that. Then everything that is left, you make a place for. It really is simple, but hard to do. There are a million excuses while unrelated stuff is in the shop. I am constantly battling the MRS to keep unrelated stuff out of the shop, but I stand firm and refuse to budge.
You probably noticed a theme here...IF ITS NOT WOODWORK RELATED... GET IT OUT OF THE SHOP! Period. Its the ONLY way you will ever be organized.