Yes. It comes together with Makehuman (also free) and needs to be installed as Blender Plugin (it is just a Python script).
You select the Armature, then on the left side you click "Load and Retarget" and then select a .bvh file.
It will try to retarget automatically, but you can select some predefined targets or also write your own mapping. And there are several more options.
I tried mapping CMU labs and Truebones to the Makehuman armature and it worked perfectly fine with two clicks. And Unity mapped the result fine to its own avatar system (which is also supported by Makewalk), MED imported an exported FBX without problems.
If you use some well known bone setup, you shouldn't have many problems, otherwise you'll have to tweak around with mapping files a bit. Important is, that the target armature is clean in Blender. I recently tried importing from a fbx exported by Cinema4D and Blender had the bones imported in a very strange (invalid) way. I wasn't able to retarget on that armature, but with other tries I went fine until now.

http://www.makehuman.org/doc/node/mhblendertools_makewalk_basic_workflow.html