Good luck. I wish that I could be as organized as you plan on. Unfortunately, that is not the case.
Just use common sense, with the most used things, the most accessable. You are on the right track with combustibles away from sources of ignition, and I would include any welders, metal cut off saws and grinders, along with the cutting torches. I recommend a METAL welding and cutting bench in a clean, well ventilated part of the shop, away from those combustibles, accumulated litter etc.
It is not too hard to run some plumbing for compressed air and electricity to convenient drops, or outlets to plug in to or attach on to. A good solid floor that does not absorb oils, grease etc., and that is easy to sweep or clean is worth the extra expense or planning. There are always lots of small, sharp metal trimmings and oil etc around a drill press or lathe if you plan on having those. Keep woodworking and metal working seperate, lots of combustibles are generated in wood working.
Two 2 X 12's is a good size for a work bench for me, but the height should be determined to correspond to your height and what is comfortable and most convenient to you. That is a variable that would not be the same for everyone.
Any vices or anvils need a very solid and secure base to mount them on, with plenty of headroom for different size materials that you may work on, as well as side room to fit large, or long objects.
Beyond that, if I haven't forgot something important, it is pretty up to you regarding what you have in the way of equipment and tools to accomodate and your personal preferences.
That is my first reaction off the top of my head, I am sure that perhaps others, if and when they may drop by, may have some other thoughts and suggestions.
Bill P.

Thanks, Bill P. I'm working up some drawings now on a base cabinet that can be a drawer unit or a shelf unit, both being the same 24" width. Not that we a re planning to move, but I'm wanting to do modular cabinetry that I can take with me if we do. All that work for nothin! No way. I'm planning on hanging the wall cabinets on a "french cleat" , an angled board screwed to the wall and a corresponding reverse angle on the cabinet so they nest together. And if I don't like where it is in realtion to the work area, I can pick it off the wall and hang to on another cleat in another part of the shop. I'm also making a solid toekick around all cabinets that touch the floor so I can sweep up efficiently. I have nine million small parts to deal with and need cubbies, drawers with dividers, or something to organize this stuff. I've gathered my welding stuff all into one corner of the shop and try various ways to arrange it for ease of use. I plan on a small spray booth and solvent venter as that stuff is deadly to me. I've been around too many chemicals in this life and have no more tolerance to it. Speaking of chemicals, I want a parts washer bad. And a sand blaster, small lathe, and roll-around toolbox.

Don't forget shelving, wiring and/or plumbing for a microwave, fridge, audio system and maybe TV, sink, etc. I'm plumbing with copper Type-L pipe for ceiling air drops at bench edges and next to the ceiling power drops.

I've also located a 50-foot air hose reel and drop cord light in the center of the shop, plus have air outlets out the front and patio walls along with power and water. Then, there's 50-amp power outlets just inside the front and patio doors for when outdoor welding will be attractive.

Finally, I've installed a Hot Dawg 45,000 Btu propane ceiling mount garage heater for those cold winter days and nights.

My shop came with workbenches and cabinets (old house with big shop).

The benches are about 30" deep. I think the deeper, the better. There always seems to be a need to keep various things on the benchtop, and you want to leave some free room in the front to work on.

I wouldn't also obsess too much about the beauty of the pine boards. Most likely they'll become scratched and dented soon enough. I prefer a harder surface than pine, like hardwood or metal. Your choice there.

The former owners put in a lot of cabinets directly into the 2x6 wall stud bays. These extend from four feet to about seven feet, and each one has a painted plywood door that also locks. They put a lot of fasterners and smaller items in these cabinets, a tradition I've continued. This is a mild climate so having the goods in the wall space isn't a big deal. Also, the rest of the wall is covered with 1/4" painted plywood, floor to rafters.

For tools, I keep them in their original cases on shelving below or above the work benches, or in a couple of large metal toolchests that are on rollers (but rarely move much).