I wrote a verlet based physics engine years ago and had similar issues. Relaxing distance constraints tended to add a bit of angular momentum in to the system. Sometimes having a drag term in the integrator was enough to compensate, but this appears to be in verlet.js already.

Another issue with defining shapes via distance constraints is that they sometimes have alternate solutions / stable minima. For example, you can smash the circle in to the ground and get it to crumple: http://i.imgur.com/UzxbKvJ.png

But, this is still an awesome demo. Good work subprotocol.