I have a little different perspective than most of you because I sit in a wheelchair. That means either I have a "set of hands" doing my work or I have friends working out of my garage. So, my tool organization has two objects:
1. Make it easy for anyone to find a tool and organize the work area for the least amount of effort to retrieve a tool.
2. Once the job is done be able to scan the tool set (and I have a lot of tools) and quickly identify what is missing or misplaced.
I am pretty ADD about my tools and about the work area being organized when work is finished. If I can't find a tool within 3 minutes of needing it I start to get antsy inside. My garage is the space in my life that gives me order and brings calm. It is an area I can control.
I won't say my organization will ever be done, but I improve it every day.
For sockets/ratchets/extensions I purchased the red cart from Harbor Freight. 1/2 drive is the bottom drawer. 3/8 metric is the middle drawer. 3/8 SAE is the upper right. 1/4 and specialty stuff (hex, torx, etorx, etc) use the two upper left drawers. Screwdriver holes are filled by torque sticks and long extensions. The top holds speeders and what I call my beater screwdrivers (Taiwanese Perfect Handle Screwdrivers). Impacts/air tools, flip sockets, axle nut sockets, and a bundle of red rags are on the bottom shelf. Popular chemicals are in the can holder (carb cleaner, brake cleaner, penetrating oil, wd40, lithium grease, silicone spray, and a squirt can w/ power steering fluid in it). All sockets are on rails.
My 3/4 inch stuff hangs on the pegboard. I'm a pegboard fanatic.
I generally find the easiest way to work is to roll the red cart to the front of the car for easy access. A gray work cart is also near by. As tools are used they are placed on the gray cart. Then at the end when cleaning up when the gray cart is empty everything should be back in its place.
As a side note if you ever get angry with people using your screwdrivers as prybars or chisels go buy a set of perfect handle screwdrivers and keep them handy. They work great as beater screwdrivers and people learn really quick to reach for them because they are so close to what they are working on.
Here is one link, but I know I have seen them cheaper elsewhere:
http://www.garrettwade.com/product.asp?pn=05R01.03 &bhcd2=1285003391
My dream project is to actually make socket holders out of sheet metal for each set of sockets. I am actually looking at a brake, shear, and notcher to do it.