Like 50 red solo cups and a roll of 3/4" masking tape. Example being you pull the upper intake off, throw the bolts in a cup, piece of tape that say "upper intake" and put it aside. This is how we do it at work and it's the best way I've found to keep track so far.
EDIT: and like OJ said above, take more pictures than you think you'll ever possibly need.
Sent from bored/stroked iPhone 4S