There really isn't a good answer for this; this is what I've recently done:
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Bought a whole mess of Stack-On brand multi-drawers and dividers (you have to buy the dividers separately). I now have for my electronic parts two 60 small-drawer units, and two 30 small-drawer units, with an extra two 30 small-drawer units for future stock.
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One of my 30 drawer units I used four rows, 6 columns, two values per each drawer - and filled them with 100 pcs each of an EIA "E-24" 5% decade assortment. It wasn't cheap, it wasn't easy - but I stocked up. I was pointed to do this by another forum member; after reading about it and understanding it, it made sense.
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For my capacitors, I bought surplus 100+ pcs each of the common sizes used on the Arduino and for common digital circuits, and filtering - nothing special there. They went into other bins.
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In still other bins I sorted out a huge variety of ICs and other parts that I have had for a long time; I also bought a ton of LEDs (red, green, yellow/amber - also white; no blue, though - need to get some blue). I have other bins with relays, small motors, small speakers, etc. Its really somewhat insane. I also have larger lidded tubs with larger component (like gear motors), as well as "tear aparts", etc.
Anything else I use my favorite local store, Apache Reclamation and Electronics, as my alternative "pay to play" storage area. Today I purchased a whole lotta various voltage regulators (7805/12/24 and 7905/12/24) and various transistors and mosfets for "scrap value". I probably got $3-400.00+ worth of stuff for about $50.00; I've been going to this place for almost 20 years though, so that helped (they even threw in a couple of small gearmotors for free!).
I bought a label maker (got it at Goodwill) and label every one of my bins; I still need to label my boxes/tubs - not all of those are labeled yet, but will be. Once I get my "shop computer" built, I plan on setting up a spreadsheet of parts and quantities, for help in the organizing and purchasing department.
The above isn't for everyone; you gotta have the room for it - if I didn't have my shop space at home (about a 100 sq ft area), it probably couldn't work - but you could do something on a smaller scale.
