There's an intriguing program called Jimmy|RIG that automaticly rigs figures. Check it out at http://www.origamidigital.com/typolight/index.php/home.html.

It's meant for motion capture but looks like it also rigs and makes joints for any figure. I never used it, but it looks like a great program.

I don't know if applys to your problem, but it sounds like it might.

Mike