@alberto
It's been a while since I played around with motion captured .bvh files but in my experience it's really not worth the pain of trying to modify the skeleton to suit your own model. You can change the scale of bones but modifying the location and rotation of bones will lead to nightmares. You will have to go into the IPO editor to correct the ipo curves to match your changes (move the quarterions etc) to get the modified skeleton to follow the pre-defined motion captured moves.
By the time you've got good results you'll know so much about rigging and animating that you are better off animating from scratch with your own properly constrained skeleton :)
I do sometimes use .bvh files as templates for my own animations eg import the bvh file next to your own rig and then you can easily see where to locate and rotate your own rig to match the moves. Great for adding those subtle movements of bones that can add that extra level of detail needed.
The key to character animation is getting the rig defined with all the IK, FK, Track To, Locked To constraints in place and then animation comes quite easily with, for example, a single controller bone moving all the foot and leg bones automatically.
This is a very good tutorial for learning rigging suitable for low poly game models. Obviously you can ignore all the facial animation shape key stuff. The tutorial covers everything from modelling the character all the way to non linear animation creation, I learned a lot from this tutorial.
http://wiki.blender.org/index.php/BSoD/Introduction_to_Character_AnimationHTH