I put ’em in a HD Freezer bag and mark the bag with a felt tip pen. It keeps ’em together & keeps ’em clean. It’s OK to stamp the piston crown, but scratches or hammered marks on connecting rods may breed cracks.
I am a fan of marked yogurt cups or similar containers. It is easy to put needle bearings and the like into them as you disassemble. I also mark with a magic marker or felt tip pen. If stuff is apart long term, I switch over to Garry’s freezer bag method. Also, when I disassemble the big end of a connecting rod, I screw the cap back onto the rod loosely, as soon as possible, to avoid mistakes. I even wash them that way.