The system I've found works best for me - given that I am woefully unorganized in general - is to put all the unique components for a particular *board* in a separate, labeled box (often a shipping box from Mouser, Digikey, etc.). Commonly used SMT resistors and capacitors in decade values and 0805 or 0603 sizes are on separate feeders for my manual pick-and-place setup and don't go into the above boxes (unless they are in a different package - eg, 1812 or 2220 capacitors, 2512 resistors, etc.). For example, 100R / 0805 resistors are on the feeders, but 330R / 0805 resistors - despite being used nearly as often - are packed with each box because they aren't a decade value.
I also include in the box the BOM spreadsheet along with the bare boards and stencil so I can easily pop out a board on demand with little fuss. The downside to this system is that I have lots of duplicate parts in each box (the aforementioned 330R / 0805 resistors, 1n4148 diodes, 2n3904/2n3906 transistors, etc.) but these tend to be inexpensive components, anyway, so not a big deal. Another downside is the sheer volume taken up by all the boxes for all the boards I've designed over the years (well, since I started using this system, which was about 15 years ago).