Solid dot at size or crosshair, in a non-printing color or on a non-printing layer in the file. Most often though, you could send a low resolution PDF with marks for position and leave them off the production file. This avoids accidental inclusion in the printed pieces for whatever reason (Murphy's Law, etc.)
Thanks everyone for the replies.
From the printers perspective, do they then print a template with the non printing layers and use it as the first piece in the stack to drill through?