Oh, I love this post. I'm a librarian who loves to organize! I can give a few tips. At least I can tell you what I do, right?
I have several systems made of drawers, boxes, glass jars....whatever I can get cheap and can label. I use one system for misc. stuff, one for precuts, one for notions and so on. The easiest way to describe it is to say the more often I use something, the closer to my sewing table it gets to live; which means the less often something is used the farther away it is stored.
Most important tip: label every box, drawer, bag, etc. in letters large enough for an old person to read (cause you'll be old and half blind before you're ready). Also important: put stuff where it belongs (cause if you don't you'll have to clean every week or so. Ask me how I know.)
A "system" is any storage set (drawers, boxes, bags, etc.) that stay together. Most of my systems have the same type of storage but in different sizes; such as small drawers on top, medium drawers in the middle; large drawers on the bottom. (Stacking as much as possible to save floor space.) Some systems have the same type, size, color so that they match.
I decide where it goes first by how often it's used, then by how much space it takes, then by whether it needs to be with (or separated from) other like items. Let's take buttons....I have lots and lots, they are used very often, they are in sets and singles, they could easily be separated from other sewing notions. Buttons are stored in small tackle boxes that can be arranged in multiple ways. I have 7-8 of these boxes: whites, darks, pastels, brights, metals, etc. I also have vintage buttons from my late mom that I keep separated so they aren't used on a whim. Those are in clear glass jars on a shelf (sort of part of the decor).
Seldom used tools go in the drawer with the items they are for. IE the pliers to put in snaps go with the snaps. One drawer is specific for "guy tools"--hammer, cutters, screw drivers, etc. plus nails, screws, picture hangers, etc. that I don't need often but I don't want to have to go to hubby's shed to search for days either. PS on tools: my guys would never touch them: 1) the tools are small (girl sized) and 2) the guys are afraid of me. :-)
If you're lucky enough to have wall space, add shelves above a system with baskets or jars (forget fancy expensive ones, go to the dollar store and buy cheap ones--they hold stuff! If you hit a sale, buy lots of the same color and size. They will look good together, and when labeled, they'll do their jobs just as well as expensive ones would.) Again, label!
I use a basket system for notions: bias tape and bias maker, ribbon and fray block, elastic and bodkins, zippers and zipper foot. My reasoning is that when I need the item, I need the tool; they're together, so I can grab both at the same time or just take the basket. If something takes two baskets, I either use a larger one or separate but the info goes on the label. Zippers are labeled neutrals and colors. Plus the baskets are kept together but the neutrals are used more often so it's on top or in front of the stack.
Cover cardboard boxes in the same gift wrap and label for patterns and magazines. I also have binders for patterns I've designed and for articles, etc. that I've printed from the web. Everything is in sleeves and, yes, labeled.
I use a peg board for thread sorted by color. I keep only the items that I used every day near my sewing machines or on the work table. I also understand that organizing is a work-in-progress. Editing and adding are part of that process and getting messy is part of creating, so it's a symbiotic relationship. lol Sorry, I may have overdone it!!!