This is my Hardware Design directory template which I found most useful.
Here is how the Directory Tree looks
Each directory contains read_me.txt file with short description e.g:
Place following files here:
– Pick and Place
– Bill of Materials (grouped by component type)
– Component reference BOM (each component on one line)
– TOP and BOTTOM VIEW (shows board outline with TOP + BOTTOM layer)
– Mechanical Drawing (Board dimensions, holes position, ..)
– TOP and BOTTOM Assembly Drawing (Component position with Reference Designator)
UPDATED! Download latest version from 11-JAN-2013 here.