In the weeks since I released the BVH conversion of the Carnegie-Mellon motion files in July, I've received a variety of email inquiries from people who quite sensibly would like to get the files to work with their preferred animation software, which typically isn't MotionBuilder. The email I've received has been interesting because it suggests that people are using a variety of applications. So far I've had multiple email inquiries from Poser 7 and/or Daz Studio users, multiple inquiries from iClone users, one from a 3dsMax user, and one person way out there at the high end using Endorphin.
Unfortunately the answer at this moment in time is "there is no general-purpose, low-cost, easy method of converting BVH files from one character rig to another". Although today you can take the BVH-converted Carnegie-Mellon motion files and use them in a professional animation retargeting program like MotionBuilder, many people using consumer or prosumer-level animation software aren't having a lot of luck making coherent animations using these files.
"Why is this so?" you might ask. It's a good question. The answer is that any given BVH file is designed to apply to a specific skeleton that's been set up (rigged) in a specific way. If you use the BVH file with its original skeleton, the animation works. If you try to use the BVH file with some other skeleton, or with the same skeleton that uses a different joint rotation setup, you'll typically get crazy animation - the arms or legs fly all over the place, for example. This isn't the fault of the BVH file, it simply means that the BVH file was never designed to work with the skeleton or rig of the new character.
The general problem is called "motion retargeting" or "animation retargeting" and is an active area of research, particularly for complex or varied skeleton setups, in the professional animation community - see for example this 2008 SIGGRAPH paper which discusses animation retargeting for SPORE.
Specifically for SecondLife use, one program that you might try is BVHacker, however I haven't experimented enough with this to know how well you can apply it to the Carnegie-Mellon BVH conversion release that I've done.
As always, if you come up with a workflow that works, something that "makes hobbyist 3D animation easier, cheaper, faster", feel free to email it my way (see the "about the editor" sidebar here for my email address) and we'll see if we can turn it into a blog post here at cgspeed.com.