Whats the standard for denoting the orientation of an LED on a PCB?
Make a pad for the cathode square.  This works even if your PCBs don't have silk screen.  If you do have silk screen on the PCB, then draw a flat on the cathode side which would correspond to the flat on the actual part.  


 
(mechanical drawing for a typical T-1 3/4 throughole LED from datasheet)

Orient all diodes in the same direction.  It reduce errors during manual assembly.  This guideline applies to other types of polarized components too.




The PCB layouts above were sketched in ExpressPCB.  Typically, the footprints for diodes that come in the libraries with PCB layout packages have some way of showing polarity.

related: How Should You Mark Your Diodes? (write-up in a free industry journal)