Modern yaw damping systems even help counteract the twisting/bending of the fuselage due to crosswinds.
Given how sophisticated the software controlling that aircraft is, I'm surprised that it can't take the last bit of 'tail wag' out of the equation.
Maybe your comment above says more than it seems. If the aircraft is so bendy that you can't stop the entire length wagging at the same time, I for one would like to see it made out of cast iron, but the BAC 1-11 was probably the last aircraft to be made thus. The damper on that was there because of the dangerous - to the newly trained on type anyway - levels of yaw/roll couple. On the 777 all this should be history. There should be no inherent wag, just the natural and often quite pleasant movements that we have all accepted for so long.
It could be the very fact that there is not this freedom of movement: computers doing such a good job of 'accurizing' the flightpath of the wings, that it occasionally leaves a residual wave that travels down the fuselage. My feeling is that something fundamentally wrong and I would bet on something like this going on.
You infer that it would be much worse without the damper. That gives me little comfort. Looking at the five or six rows of people in front of me all be doing some sort of bizarre Mexican wave, caused by the lightest of chop...and I mean light, how could this happen in a well deigned airframe?