I can only tell you what we do with it in 3D Max.
There you can have the ragdoll physics in your rigging and you can also have a "normal" biped behavior, and then you can mix the two. So, for example, as a person is hit by a log (this is an animation I did so I'm pretty familiar with it) the body reacts as a rag doll but then the human flails their arms as a real person would in an effort to regain their balance. By varying the percentage of the mix you can achieve the "real" look.
The percentage controls the limb -- imagine the physics of the arm being knocked backwards by the log, and then attempting to reach forward. The forward reach is modified to whatever degree is necessary to look natural.
All of this is much easier in practice than it is to describe -- we simply keyframe the "normal" reactions and then let the ragdoll physics simulation run and then blend the two, judging visually how much to add of each. Otherwise, as I said, it looks as if the human is unconscious (which is all right sometimes, but not usually what you want).
Or another example -- a person falls but attempts to turn their body to land on their feet (but then hits and crumples further). Once again, you need the basic motion of keyframing the attempt to stand, mixed in with the ragdoll physics of the fall.
If you like this kind of thing there is a 3D package called Endorphin which has a trial (free) version for playing with. Here's the web site:
http://community.naturalmotion.com/
You could conceivably produce the same sort of movie animations that Gary is using with Poser and bring them into AS for rotoscoping. If you really like this sort of thing you can waste... um, spend a whole lot of time playing around with it. I think it's something everyone goes through once in the phase of 3D (kind of cool to "throw around" a person who can't actually get hurt). After a while the novelty wears off, though.