Reference, when used in terms of graphics cards can mean several things. A reference style GPU usually means that the card is presented as the GPU maker had intended (Nvidia and AMD).. this includes everything from the PCB, layout of the components and the heatsink/fan.
A non-reference cards is when the card manufacturers (like Sapphire, EVGA, HIS...and so on) make changes that deviate from the original design. These changes can be something like a better heatsink/fan design, overclocking, changes to the PCB or any other changes that they see fit to make.
The nice thing about reference model gpus is that you are assured a certainty level of quality becuase they are built to the gpu companies requirements. In many cases all the way down to specific components on the gpu. Non reference gpus can be built above or below original quality levels. Luckily normally they are an improvement over reference but some companies have been caught using cheaper components on their non ref gpus in the past. Not cheap enough to effect day to day performance but overclocking suffered.