Excellent question! the z79 chipset supports Quad ram access, so 4x4Dimms would have better performance out of the box than 2x8.
That said, 2x8 gives an opportunity for easier upgrading in the future.
Also, I agree whole-heartedly with Alex Smith, both on the speed recommendation as well as the ram choice. Interestingly, even if you did need faster ram in the future, I owned a triple set of Corsair Vengeance 4gb @ 1600mhz, and overclocked it just by adjusting timings to 2000mhz stably.