Originally Posted by Guano11
This may seem so obvious, but it was a revelation to me (and I thought of it myself): As I strip the bike of tanks, plastic, fairings, etc, I will keep the fasteners in the appropriately labeled bins of a fishing tackle box.
Another variation on keeping fastners organized:
If you have a part that's attached with multiple fastners of different sizes and lengths (such as a side case), draw a picture of the part on a piece of cardboard and poke holes where each of the bolts are positioned. As you remove the part just push each bolt through the cardboard drawing where it belongs and set the cardboard aside. On reassembly, you now have a nice picture of the part and you know exactly where each fastner is supposed to go.
I'll also take a digital pic of any complex assembly that I have to take apart if I think there will be questions when I reassemble. You can put the pic on the computer and zoom in on the parts in question to make sure you have things correct. Take many pictures from different angles and of all relative positions of the parts. If you don't need the pics, just delete them later.