Very useful post Marketing Guy.
Am I right in saying that it was the sheer volume and content/structure of these pages which made things obvious to the Great Google?
We have scientific clients who may publish new research, or who take genuine advertorial on their latest development on science websites to promote their business. By 'genuine' I mean that it contains useful information to their community - even if it is (and must be) substantially the same content as this kind of info has to be accurate. Will they get hit if these advertorials, press releases etc. appear at roughtly the same time on a range of science sites linking back to the clients site?
If so, then I think this represents the genuine concern of those who are legitimately trying to market their businesses online and get put into the same pot as others who seem to be clearly trying to manipulate Google on an industrial scale.