[hyperion2010]

If we wind the clock back far enough couldn't we explain this if the original matter that went on to form the black holes originated from blobs of matter that were affected by the same local forces? Then we just wait long enough and things that were next to each other in the distant past now reside long the dark mater filaments? Given the angular momentum of these suckers I'd guess that it is pretty hard to significantly change their axis of rotation even over a couple billion years.

[Tloewald]

I don't see how that explains the axes aligning along the filaments. It might explain the axes being aligned.