I think I have my shop fairly well organized.
I use little bins for all of my bushings. I now have 6 of them. They all hook together, and each is labeled with what is in them.
Next, I put all my kits into bins, and then laminate the instructions and put those into notebooks with tabs.
I have all of my tools and most of my sandpaper on a rolling cart I built next to my lathe.
Next to this cart I have a cart for the polishes and other stuff I am 'currently' using. Inside this cart, accessible from the other side, I keep all of my mold making supplies.
On the other side I have two rolling carts, one I have more tools and then tailstock items, the other I have my grinder so I don't have far to walk (two steps) to sharpen my tools.
In front of my lathe I put a peg board wall and keep all of my bulk polishes there. I also too a little piece of plywood, pounded some finish nails into it and that is where I put all my blanks ready for turning.
Over by my drill press I took another small piece of plywood and put all the drill bits I use the most in that. As you can see from the picture, I need to expand it a bit. On the outside I put a metal magnetic strip and that is what holds all of my drill bits and pen mills that I haven't taken the time to organize yet.
I also made another rolling cart for my 'casting station.' This is where I keep all of the stuff I use for casting resin blanks. I covered the cart with free corian and white (crap, can't think of the name right now, thin white stuff you get at Home Depot/Lowes.)
I put my bench sander, by Grizzly wet slow speed grinder and my little HF buzz saw (great for cutting tubes) just to the left of my 'pen finishing station.'
And I turned my router table into a dual purpose table by outfitting an MDF top for it, and it now holds my little Rikon I just got on sale at Woodcraft, and I use it to buff and turn other stuff as well.
Next to that are my two tool chests (one I inherited from my Dad) for the other tools in my life. (and next to that are my son's tires for his car. Ugh.)
I made my last remaining wall into my "wood wall." Using shelves and open boxes to hold all my blanks and other stuff.
And lastly, since I do other stuff as well, I got these from HF when they were on sale for $59 and put all my screws, nails, and various other odds and ends in them.You can also see my small fridge for the CA glue, the shelves I built for the batteries for my cordless tools, etc.
As you can see from the pics, it's still a garage with garage type 'stuf' all over, like an odd air conditioner, bucket of sale, brooms, shovesl, tree timmer, etc.
But these are just some of the things I've done, and most of them are homemade non-expensive stuff. HTH.