In the strictest sense of the word 'reference', what KC says above is true. Same cooler, same components, same PCB.
However, in the parlance of OCN, you'll often see people use the term 'reference' to specifically refer to the PCB ... whether or not the 'layout' of the components on the board meets the reference spec. This is important for water cooling folks in particular, as it affects whether certain full-cover water blocks will fit properly on the board.
Although it's not 100% guaranteed, it's pretty safe to say that when a new model first comes out, say the GTX680, ALL the cards that are out there were made in the exact same factory in Asia, and all the brands are just slapping their stickers on them.
Over time, however, the first run of 'reference' cards will be sold out, and then the ones on the market will start to vary in terms of who makes them.
Some will be made on 'contract' in various factories, and brands will stick their name on them. Others are actually made by the brands themselves (i.e. the factory has their name on the sign out front), although there's not very many companies that have that kind of capacity of their own. In the nVidia world, I believe the companies that legitimately can are Asus, MSI, Gigabyte, and Palit/Gainward (and perhaps Galaxy). The rest I believe strictly contract the work out and 're-badge'. I may be wrong on that though.
Regardless, all 'reference' cards should be, for all intents and purposes, identical, regardless of who makes them ... however, they may or may not actually be all made by the same factory.
So to some people, when they say 'reference' they just mean the PCB/layout is 'reference', and to others, reference means the whole shebang including the cooler.
Edited by brettjv - 3/30/12 at 8:59am