EVGA and ASUS only offer the reference design in those cards, MSI has the twin frozer which is supposed to be a big improvement so I would go with MSI, but if your going to get the reference design just get the cheapest because other than some stickers they are identical.
EVGA has amazing warranty and support but ASUS can sometimes be quite a bit cheaper (though I don't actually think that's the case on the 400 series cards). I don't know about MSI graphics cards at all.
They all use good quality components, so the difference is in the heatsink. The MSI has the custom heatsink to lower temperatures and noise, but exhausts heat inside the case. The reference EVGA and Asus exhaust heat outside the case.
That's the one I would go for. It is supersilent with an Arctic Cooling Acelero Extreme cooler. I also like what they say about their "binning" process:
GIGABYTE GPU Gauntlet Sorting
Gigabyte’s proprietary database analysis system evaluates the GPU core engine, shader engine, and memory, and selects the qualified GPU processors for upcoming maximum overclocking ability and stability test using proprietary professional testing toolkit and Graphics benchmark (FurMark and 3DMark Vantage). Final power switching and stability test will pick up those GPUs with the best power efficiency and lowest power consumption, which are qualified for the Super Overclock Series. Thus, the Super Overclock Series have been factory overclocked at optimal stability point (Super OC point), an exact balance between high frequency and efficient power consumption.