The orientation of the interferometer arms at both sites are approximately Northeast-Southwest and Nortwest-Southeast, though I assume that, on account of the Earth's curvature, no pair of arms is exactly parallel. Is there a preferred orientation for the instruments, and is there a benefit in having them in (approximately) the same orientation? My guess on the latter issue is that if an interferometer has blind spots, it is better for those at both sites to be aligned (or at least overlap as much as possible), as a blind spot for one is a blind spot for the instrument as a whole.
Answer
For the German GEO 600, I happen to know that the orientation (and the fact that the two arms do not form an angle of $\pi/2$) is mainly due to building site constraints.
As LIGO seems to be in the middle of nowhere, this might not have played as big a role. However, it seems that your assumption that most interferometers have a similar alignment is wrong - see here: http://www.ligo.org/scientists/GW100916/GW100916-geometry.html - the orientation changes actually quite a lot.
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