Orientaion Flat on Semiconductor Wafer
As stevenh says one of the purposes is to ensure correct orientation during handling.  The other reason is to indicate the crystal orientation of the lattice and the wafer doping.  From BYU's cleanroom website:


  Wafer Flats
  
  Purpose and Function
  
  
  Orientation for automatic equipment
  Indicate type and orientation of crystal.
  
  
  Primary flat – The flat of longest length located in the circumference
  of the wafer. The primary flat has a specific crystal orientation
  relative to the wafer surface; major flat.
  
  Secondary flat – Indicates the crystal orientation and doping of the
  wafer. The location of this flat varies.
  
  For large crystals no flats are ground. Instead a notch is machined
  for positioning  and orientation purposes.


The crystal lattice is defined by how the wafer grew from the initial seeding.
It is important to cut the wafers along the crystal lattice if you want a clean break.