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Usually non reference cards have a different board layout. These two seem to have the same board layout (from the back pictures), just a different fan location on the cooler. As for cooler, I trust EVGA to design the best cooling for the card, especially if they are standing behind it with the Lifetime Warranty.
I personally like having the fan at the back end of the card like the non ref one does; I had a pair of 8600's in SLI that had the fan in the middle, and the top card was always hotter and eventually burned out. I still believe that it was due to the fans being placed directly over the GPU of the card below it.
IMO, EVGA LTW trumps all! I haven't lost an EVGA card yet, but I know a couple of guys that have, probably from seriously overclocking them. The cross shipping program on the LTW cards is great. Supposedly the support guys are top noch as well, and don't send you through a bunch of scripted crap if you seem to know what you are talking about.
Based only on the pictures, I prefer the non-reference design. The reference design seems to have the potential to trap hot air at the back of the card, or send some hot air back into the case.
The hole point should be to exhaust hot air outside of the case. The non-ref card looks like it would do better.
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