One method is to create storage for everything. In this method, all tools are in cabinets or drawers and must be brought out for a job and put away afterward. With a limited work surface area this allows for any job to be set up on it and then later cleared.
Another method is to set up work areas around each machine with all the accessory tools that relate to that tool. With this method the project moves from work station to work station. This method will require more space but a job can start and finish quicker.
Most of us are constrained in some way by space or facility layout. So each solution will be specific to our physical plant, the kind of work we do and the way we like to work.
For me, I want a combination. Since I have a small 1 car garage I will need flexibility which means I will have things on mobile bases. But I also want work stations so I will design and construct storage for accessories that will also be a part of these mobile work stations/machines. I will need some fixed elements but most things will move, including work and layout benches. I will also have to separate functions and put woodworking in another structure. The garage will be automotive and metal working. This setup means I will have to configure the shop for whatever job it is that I want to do. Each workstation needed will have to be pulled out including work bench surfaces. But hand tools and accessory items will be right at hand for that task without removing them from storage. I will have racks and shelves right at the machine or bench. Grab a tool, use it and hang it back up. This will work for making metal or wood items, but automotive requires moving the tools to the vehicle. This will be necessary since there is no inside space for vehicles yet. So a service cart and hand carried tool boxes or buckets will have to do for now. Organized by task. Electrical, cleaning and detailing, welding, general wrenching etc.
It's gonna be fun using all the ideas from this group to design and organize things. It won't be a shop with clean finished lines and no tools visible like some on here where all you see is floor and cabinets. But everything will have a place and most tools will be behind doors for protection from dust. Go to a work center for say a drill press and throw open the cabinet and there are all the fixtures and drill bits and chucks and such.
The advantage of small spaces is that you don't need duplication of features. Everything is close at hand. And the worker and his work can move easily from place to place.
I worked as a machinist in a 2 man shop where all surfaces were covered with a jumble of tools and materials all the time. It was horrid. As a newbie, I had to spend countless time looking for each tool or part. This was because I couldn't easily just see and pick up just the right size mill or tap or reamer. But the owner, who could tell size just by feel, also spent much time looking for things. I eventually learned to keep my own stash of basic tools and tooling in my own specific storage places, and to return them there after a job. We finally spent the better part of a week sorting and sizing and storing things. But the secret is really what you do AFTER that. Without the discipline to return things to their place of storage, it all goes to hell again. Everything has a place. Everything is labeled. Nothing moves to new places. You get trained where everything is. You put everything back after use. End and start of day the workbench is clean. Beginning and end of job the workbench is clean. A place for incoming materials. A path for materials to be processed. A place for finished products to be packed and shipped. Beginning of job, look at part to be made, get materials and tools and assemble on bench. Process materials and use tools to make part(s), going from machine to machine. Finished parts to shipping. Tools back in their spots. Happy worker.