Continuing on the Baking theme of my last 2 posts, here's how to bake Physics to an armature. Check out how to set up the physics here: http://cgcookie.com/blender/cgc-courses/creating-ragdoll-rigs/
Layer 1 = physcis sim, Layer 2 = Rig with bone constraints that follow physics objects, Layer 3 = mesh applied to rig, Layers 11, 12, 13 = camera, lights, floor.
In this simple example, 3 bones, follow 3 objects bound by physic constraints. Play the sim, Alt-A, the bones follow. The sim object Sphere.009 is keyframed to twist and rotate, driving the physic sim on Sphere.008 and Sphere.007. Note for this to work Sphere.009's Rigid Body modifiers needs "animated" option checked. (Instead of keyframing the object to twist, it could be drivin by a bone as well, the caveat being, parent the object to the bone, not the armature with weighting)
Each bone except the root has a "Copy Transform" Bone Constraint, making them follow the sim. This file is baked but, once you are happy with your own sim, select each bone in Pose mode, in the Pose menu click Pose - Animation - Bake Action. From the Bake Action menu - All frames, Only Selected, Visual Keying, Pose and Ok to bake. This will create a new action with all the keyframes. To see the bake, disable each bone constraint to see the bakes action isntead. Don't expect perfect tanslation, close is good here.
Uses: Imagine a character's accessories bouncing around while they ride a horse. Instead of keyframing, you can capture realistic bouncing and swinging from the sim instead.