The essence of what we are talking about in this thread is Kindergarten Lesson #1.
We do many things with our shop, and penturning is only one aspect of that. The goal is to keep related items together in small, well-organized and labeled containers. Group related containers into larger containers, and organize them well on shelves, cabinets, or whatever space you have. Put away everything as soon as you are done with it, so you can find it again. Do not start anything until the tools from the previous project are clean and put away.
I admire the many organization examples above, especially the wonderful custom storage that many have built for themselves. We do not have fancy storage for our shop tools and supplies. Our cabinets and shelves are old and used, picked up at surplus/salvage sales and swap meets. We have old metal shelves and metal cabinets, an old kitchen cabinet mounted to a wall, and a used 12-bay elementary school locker - a good match for our needs. In my opinion, the smallish size of the kitchen cabinet and locker spaces are just right for keeping things organized at the right level.
Storage containers themselves are mostly used or repurposed. In addition to making use of old plastic and cardboard boxes and containers, we also have a collection of Rubbermaid tubs and lids in various sizes that help organize stuff. We keep a stack of various size plastic tubs in a shed. The storage tubs are constantly used, reused, and repurposed - going back and forth to the shed all the time.
Tools and supplies should be well-organized and well-labeled. The way my spouse uses her Brother label maker, I wish I had bought stock in the company years ago.
Working down, for penturning, most supplies are in an upside-down cardboard box lid from a copy paper box, which is a good fit for one of the lockers. Inside that box lid are old upside-down cylindrical CD storage lids. One holds glues. Another holds the bushings, each set in their own labeled original envelope. You get the idea. You pull out the cardboard box lid and the organized supplies are ready to go. Other penturning/woodturning supplies (wood and plastic blanks, pen kits, other non-pen kits, etc.) are grouped in Rubbermaid tubs that are stacked on a file cabinet. I pick the right tub from the stack, pull out what I need, put the stack back - easy peasy. Pen kit instructions go in a file cabinet. I throw away the duplicates, and the new ones go in the file folder. We keep sheets of sandpaper in the file cabinet, too.
Penturning Organization Rule #1:
Only one set of bushings is out of its labeled original envelope at a given time.