I have several methods depending on what it is. My shop has been in the basement of my house for the past 10 years, and there has been no built-in storage, no on-wall storage and no workbench to speak of, so everything I use gets taken out at the start of a project and put away at the end. I use the Stanley/Stack-On/Harbor Freight parts organizers with the little removable bins for most of my small parts and hardware, plastic shelf/hanging bins for some hardware items, and Rubbermaid or Sterilite stacking totes (10-12 gallon size) with labels on them for larger items or specific trades. So all of my plumbing fittings, for example, are in a lidded tote labeled "Plumbing Fittings". That has a couple of smaller bins inside of it, one with copper/brass fittings and the other with misc. stuff like teflon tape, pipe dope, brushes, etc.
I try to visualize the end use of an item, and the first word that comes to mind , is the bin that it rests in. A light switch would be in the "Electrical" bin, in the sub-bin with switches and receptacles. There's also sub-bins in that one for breakers, lamp parts, and wall plates, for example. Wire nuts and small items are in one of the aforementioned Stanley or HF parts organizers, and those are all labeled. I don't want to have to look for something for more than a minute or two, so everything is well organized and labeled. My hand tools and power tools rest in a couple of vintage 4-drawer file cabinets and a small Kennedy roll-around box.
I do have a half-assed workbench in my new garage, and even the piles on top of it are organized until I can get the garage finished and move my organization out there. I don't know what I'm going to do with all the possibilities in a new garage - I've been living without permanent storage for so long, but my current system seems to work. It was always intended to be temporary, but I can't imagine something different at this point. At least the bins, organizers and totes will sit on shelves and cabinets dedicated to storage.