While I begin to work through the process of attempting to get Google to restore the cgspeed Google Sites content, which contained a variety of notes and explanations about the different filesets, I'll post links to the various conversions here, in separate blog posts.
This dataset is the second Motionbuilder-friendly release. In general, for Motionbuilder use you probably want to use this dataset, rather than the original conversions from 2008.
From the README file for this release:
I released the original Motionbuilder-friendly BVH conversion in 2008. This 2010 release is very similar, but has a few minor adjustments to some of the joint rotations of the frame-one T pose which are intended to make retargeting look slightly better in most cases. This 2010 release doesn't touch any of the other frames and doesn't change the Motionbuilder-friendly joint naming convention of the 2008 release. In general, you'll probably want to use this 2010 release.