I get a package of 3x5 cards, cut them in half and a whole bunch of baggies.

I use a sharpie to write down on the card where the thing goes, etc. then put the index card half in the baggie with the part.
Also take pictures.

Pro tip: write down on the index cards as if your mom was going to re-assemble the engine in 3 months. It will help you make clear instructions. This works!