Quoted from xTheBlackKnightx:

By type and commonality.
Common everyday parts stay "on the rack".
Excess common are placed in bulk containers under machines.
Game specific parts stay "in the boxes".
Electronics and associated ICs should be separated from all other common parts to prevent damage and oxidation in closed air sealed containers, not bins.
Fuses should be in their own "flying fishing" container.
Same organizational method applies for tools.
Most don't need oscilloscopes on a daily basis.
If you keep having to reorder things that you cannot find, then you need to upgrade your storage facility methods.
Bins, tupperware containers, masking tape, and black sharpies are a fairly inexpensive option.
This precludes the need for some "giant warehouse shop" to do work.