Having a typical real-life (small) garage I am a fan of baggies, file cards and sharpies for labels and a assortment of tupperware-style containers.
You can also dedicate a digital camera and make tons of photos, then put each set of pics in to its own named folder.... fuse block - right front shock mount - fan mount screws - etc. You don't have to print anything, just note the folder on your file card that goes in the baggy. You can refer back to them when re-assembly time comes.
While in California for the Werks Reunion we visited Canepa on Saturday morning, if you've never been you must make a point, yikes, it is incredible.
They were doing a ground-up nut-and-bolt restoration of a Daytona. Every small part was bagged, labelled and stuck to the walls of the work area. Tables held each major assembly, all laid out in order.
Every single work station throughout Canepa was the same, spotless and in perfect order, and of course they have tons of available room.
It was pretty inspiring to see in person. Sorry for the lousy cell phone pics.
Good luck!