My dad has a beautifull little stamping kit with letters and numbers just for this sort of thing. I still haven't got one, or stolen his yet, but I really need it. I find a black sharpie written on the metal after it has been cleaned off with a bit of solvent is good.
However, the king of easy marking is a white-out Pen, the type with the roller ball tip. It will mark on anything short of grease and if you clean the area first you can still see the white marks on future teardowns. White shows up great because in a car everything used is dark. lol

Former owner of '99 CSVT - Silver #222/2760 356/334 wHP/TQ at 10psi on pump gas! See My Mods '05 Volvo S40 Turbo 5 AWD with 6spd, Passion Red '06 Mazda5 Touring, 5spd,MTX, Black