For every part I take off, I put the bolts, clips and other small pieces in a zip loc bag and label it. If there's something unique about the assembly, I draw a little picture of it and put that in the bag. I have plastic boxes (used to ship small items to parts stores) that are labelled for major sections of the car (e.g., firewall) and a put the baggies in the appropriate box. As I accumulate the replacement parts, I put them in those boxes too. When I'm ready to assemble, everything is where I need it. (Well; at least that's the plan. It works most of the time.)
