4x6 plastic bags (ESD or plastic depending on the parts) labeled and stored in 0.30 cal ammo boxes.

My labels come from a custom part numbering system. How you identify parts is up to you. I use partsbox.com as an inventory system.

You can drop dessicants in each box as well to keep the humidity down.

https://www.harborfreight.com/030-caliber-ammo-box-63135.html

https://www.amazon.com/HRX-Package-Antistatic-Resealable-Electronic/dp/B076CXTSX1/ref=sr_1_3?keywords=esd+bag+4x6&qid=1689554901&sprefix=4x6+esd%2Caps%2C86&sr=8-3

I have some of those ammo boxes (all full atm) - and I love them.  Will consider.

I don’t think I’ve ever had a completely clean working station but over years I’ve just found a way that works for me , repetitiveness is key to organisation. Good Luck

i have a modular sorting box system, specificly designed for SMD. It is 3D Printable and can be adapted on any part of a manufacturing process or workbench. It is also configurable in size, so you can also accomodate trough hole components and/or even enclosure and mechanical parts. 

In terms of spilling, each box has its own hinged lid (unlike most of the shelf sorting boxes). 

https://hackaday.io/project/191635/gallery#1f05692a619401723bfb82931619b6a3

I'm interested, but the project goes to a 404!  Did something happen, and is there a thingaverse for it?

AIDETEK BOXES
This revolutionized my storage.  
You can fit 144 parts in the space of a hardcover book, and pull part's directly from it for assembly.  They are beautiful.  

I have my "jellybean" parts (resistors, caps, 324's,1117s,leds, etc in a couple of these, for anything project specific I just keep the digikey bags in the shoebox sized clear plastic containers you can get from any dollar store/ebay/amazon

Anything I'm likely to access less than about 10 times I keep in the original bags, used to use three ring binders with sleeves for cards/coins but never found something well sized for smd parts, I just use a box per project now as it lets me fit bigger parts too.  If it takes a lot of effort per part, unless I use it a ton I usually won't bother with anything fancy.

For tracking I just have an excel sheet. Every time I've tried to use a fancy program or database or something it's been a ton of effort to set up and when something different comes up it either can't deal with it or would require a ton of work to adapt the existing system.  If you do that sort of thing a lot maybe, but honestly just a spreadsheet is good enough ™️

For E12 series components check out https://www.aidetek.com/mm5/merchant.mvc?Screen=PROD&Store_Code=A&Product_Code=BOXALL&Category_Code=Encl

These boxes are excellent.

I’ve also been accumulating SMD parts and felt like my lab was overflowing with parts bags.  I started using trading card sleeves and three ring binders for consolidating and organizing semiconductors.  The sleeve compartments will hold 2x3 inch ESD bags.  I transfer the parts from the large Digi-Key or Mouser bags into the small ESD bags and label them with a fine point sharpie or label maker.  Binder tabs work well for categorizing.  It’s amazing how many parts fit in a small binder!  One downside is that transferring and labeling is pretty time consuming.  

These storage books are pretty good for resistors and capacitors:
https://www.adafruit.com/product/520

I am using the project boxes approach and it is breaking down. I have a lot of replication. My first thought was to develop an inventory database of component usage by project. That would bridge about 80% of the problem. It is also a non-trivial piece of code to write. Maintaining the "extra parts" that don't show up on the bill of material inventory gets messy too.

My CAD system spits out complete BOMs for each board or harness as a .csv file. One way to find stuff in the project box system is by grepping the top level work directory to identify which projects use a specific part. Far from optimal, but it helps.

Sorry that I don't have a solution yet either...