A graphics card that is referred to as "reference" is basically the card that nVidia or AMD ship from the get-go. It comes with their cooler (almost always a "leafblower") and a standard PCB design.
Manufacturer like EVGA, MSI, ASUS and Gigabyte can then release cards that still use the reference PCB design but with an attached custom cooler, or release a custom PCB with perhaps better or more functions as well as a custom cooler. Some even come with waterblocks.
As an example, here is the reference GTX 570 as it was released initially by nVidia: http://www.pbcentral.com/columns/hil...GTX5703qtr.jpg
Here is the PCB of that card: http://www.techpowerup.com/reviews/A...ages/front.jpg
Here is ASUS take on the GTX 570 with their "DCII" cooler: http://images.pricerunner.com/produc...1280MD5%29.jpg
And here is the PCB of that card: http://cdn.overclock.net/e/e0/e0a512..._DCII_pcb.jpeg