A couple of people mentioned taking digital photos. I'm currently restoring
a harpsichord (mechanical/cabinetry repairs plus detailing and refinishing),
and I've taken several hundred pictures of it already.
The small hardware goes into those little sealable plastic bags with a label
written on it in Sharpie, e.g., "music rack guide, left". Those get put in
a drawer so they don't get kicked under the benches.
The keys get numbered left to right on the undersides in pencil and put in
Large hardware (hinges, etc.) I mark using white "gaffer" tape (a strong,
cloth tape with a no-residue adhesive) and a Sharpie. It comes in rolls the
same size as duct tape. You tear off two or three inches, fold it over
itself to leave about 1/4 inch exposed adhesive, and stick it to the part.
Then write on the tape.
The large wooden pieces get marked in pencil where joints or attached
hardware will hide the marking. I never mark in pencil on a visible
surface; the indentation will still be visible even if the graphite wears
off. I photograph every part at several steps during disassembly.
In extreme cases I draw a sketch like an engineering assembly drawing, with
indications of the grain of each piece, so that I can identify it again in
the correct orientation. When all else fails, wood grain is fairly unique.