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I have a (bike) toolbox. It isn't the most glamorous steel-trayed rolling magic machine, but I can put it in my car and still do everything I need.
However, about 60 percent of its' space is taken up by spare parts. They're inescapable, and sitting in old ziploc bags of varying quality in the bottom of my box. Things that you're never going to sell, and always need to repurpose, bodge or fix other bikes.
Headset / stem spacers and top caps.
Brake adapters, bolts, washers.
Cleat hardware.
Bleed screws, clamp spares, pad holders.
Cable end caps, barrel adjusters, spare inner and outer cable.
Is there any magic or better way of storing these? Some kind of seperated hard-topped case? Something that might even go in the base of my toolbox but take up less room than the shitshow there is there now?
Another box? 😉
Or, in my case, boxes. I've been sorting out my various spare parts and selling them/giving them away.
These sort of thing are good for spares, but I can't see his anything will take up less space than what you currently use.
Or

There are loads of different sizes in this style
Ive got a couple of flip top bait boxes for mine. Can see where everything is from the outside.
Then larger stuff goes in ziplock bags in a couple of larger boxes.
Little set of plastc drawers for all the little bits.
Some ikea boxes that also take a matching tool tote for the rest.
The fatmax things are great boxes but too big for small parts sorting and not big enough for some parts.
Some IKEA boxes that have a removable 'tool' tray at the top.
Then parts are either loose if they're big, or in old plastic takeaway tubs for smaller bits, i.e. a tub for headset spacers, another for brake bolts, etc.
It's the Samla boxes & trays...
https://www.ikea.com/gb/en/p/samla-insert-for-box-11-22-l-transparent-50102973/
And yes, as above, a set of little plastic drawers for all those tiny bits.
As above, one of my lockdown jobs - very satisfying...
https://www.screwfix.com/p/stanley-sort-master-organiser-set-3-pieces/2690d
There are so many different parts in my garage I've only separated suspension and brake components as they need to be clean and away from any contamination. Everything else goes in a box. And another box and another....
Got a few sorting out boxes and I cant fit everything in the compartment so it drives me nuts
These organisers are giving me a hard on.
The sort-masters look the business; the fatmax ones would be great for small stuff but useless for, say, a brake caliper adapter.
Also, now I desperately want one of these:

Another box? 😉
Or, in my case, boxes.
And so on until you start needing another shed.....
I really need a clear out.
the fatmax ones would be great for small stuff but useless for, say, a brake caliper adapter.
They are plenty big enough for that. Are looking at it on a phone screen? You can even take out some of the pots to make a much bigger section