I have a few compartmentalized containers that I use for my common nuts and bolts - the metric ones I keep going back to. Another cool little box has four drawers that are all split up, and that's my race pack. It has one drawer for electrical bits, one for rivets, one for a selection of "uhoh" nuts and bolts and one for basic track spares like spark plugs, a sway bar end link, zipties and the like. This little box has a handle on top so it's easy to pull off the wall and toss in the truck when I'm heading out to the track. It's come in very handy.
On top of that there's one of those sets of clear drawers that is used for various bits like SAE nuts and bolts, grommets, machine screws, etc.
One of the biggest helps is a collection of ziplock bags. A big collection. When I'm disassembling a car and I run across specialized fasteners, they get put in a ziplock bag which is then labeled and put in a box with the other bags. That way I can easily retrieve a set of driveshaft bolts from a Camaro (for example) without being concerned that they may have ended up mixed in with my MG fasteners. The zombies have a hard time disorganizing the ziplocks, it's proven to be a really good system.
Each project car has its own shelves, so Land Rover parts don't mix with Cadillac parts.
And of course, there are a couple of coffee cans. I take them and sort them once in a while to replenish my various stores. I'm not inherently organized, but trying to juggle so many project cars at one time has forced me to develop some good habits. I also end up doing a major re-org of the garage about once a year in order to free up space and ensure everything is accessible. It takes a bit of time to do, but I save time overall as I never have to hunt for things. Being organized saves time, it doesn't take it.
Square left in 50 caution ocean!