You don't have to keep everything. Decide which parts are too cheap and easily replaceable to bother with, and throw them out.
Pre made resistor and capacitor kits are a nice way to keep a selection on hand that's pre-organized for you.
Lots of people are suggesting 3D printed bins but I'd recommend something anti-static, for example:
https://www.techni-tool.com/product/429BE9038-554-4ESD?srslt...