Get the reference card if: You have a case like Silverstone FT02 or Raven series that has large intake fans on the botton of the case and verticly mounts the card to blow air out the top.
Get the reference card if: You do not care about overclocking beyond 1150mhz and don't mind the sound of the reference fan @80% (its not overtop loud but noticeable)
Get the reference card if: You want to run SLI or Tri SLI and vent the hot air out of the case.
Get the aftermarket cooler if: You want to overclock beyond 1150mhz , have average airflow in your case and need the extra cooling, want a quieter card as the fans wont have to spin up as high to achieve similar or lower temps, just want the one card and want to get the most out of it.