the main benefits of the non reference designs are.
better cooling, blowers aren't great imo, and are generally loud compared to aftermarket fans provided by the likes of asus, msi etc.
better overclocking, msi gaming editions and various others will/do have a second power connector, it was mentioned by several testers that the single 8pin was not really enough to get decent overclocking headroom, adding a second power supply will up how high you'll be able to hit.
generally the non reference cards overclocking better than the reference designs, due to the better cooling and power solutions etc, as well as being cheaper.