Sauerbraten supports ragdolls for skeletally-animated models -- currently only MD5 models. These are specified by a ragdoll config file that is included in a model's config file.
Downloading the Editor
The ragdoll editor can be downloaded at http://sauerbraten.org/lee/ragdoll.tar.gz.
Using the Editor
See the included README.txt for basic information on keybinds for editing. Some additional stuff:
The savecfg/writecfg (*) command writes a sauerbraten-readable ragdoll.cfg file. Do this when you are finished. (*): some discussion arose as to which is the correct command to use, see here : Posts 13 & 14 on http://cubeengine.com/forum.php?action=display_thread&thread_id=2029
A useable ragdoll needs to have the model's joints bound to spheres (and triangles) in the ragdoll. /bindjoint (J) will bind the currently selected joint, sphere(s) and triangle. printjointmap gives some details on current binding.
You might want to place spheres exactly on joints. After doing so, to select one or the other you can use the toggle visibility commands (F5-F8).
The editor will load the quicksave file automatically. To load a new MD5 model, use loadmodel NAME. Then do quicksave (minus key, left of the equals sign) and it will be loaded automatically next time you run the editor. Use quicksave/quickload as you work for efficiency.
Sauerbraten's ragdoll algorithm was based on an article by David Rosen, Character Physics based on Newtonian Particle Simulation with Angular Constraints.