A favorite ploy of denialists of various stripes (vaccination, global warming, evolution...) is that scientists are engaged in a sort of conspiracy to silence dissent. Given the pretty widespread belief that rigorous internal critique is at the core of the scientific method, can scientific conspiracies really exist?
Unfortunately, the answer seems to be yes - though none of the above are likely examples. The most prominent contemporary example seems to be the great "saturated fats are evil" myth. Nina Teicholz has traced the story in her book The Big Fat Surprise: Why Butter, Meat and Cheese Belong in a Healthy Diet, which she is currently flogging in various venues.
Of course this was not a conspiracy of deliberate deceit, but of true believers. Their is very little evidence that Ancel Keys or any of the others propagating this myth were deliberately selling something they knew was wrong. Instead, they believed the idea so passionately that they discounted contrary evidence and relied on very dubious supporting data. Even the sugar and vegetable oil companies who jumped aboard with both feet and boatloads of cash probably thought they were during mankind a favor with their low fat foods, margarine, and other products.
One enabling factor has been the difficulty and expense of doing controlled nutritional studies, so almost all data must come from epidemiological studies. One strong piece of evidence, however, is the fact that overall, Americans have drastically reduced their consumption of saturated fats, while getting fatter and more diabetic. Also, the evidence that saturated fats are not the bogeyman has gradually accumulated and a critical analysis of the studies portraying it as such has found their severe weaknesses.
So how about those other conspiracy candidates? The big difference is the quality and quantity of the evidence. Evolution, vaccination, and human caused global warming all have all have ample evidence and detailed models of action, something that the saturated fat hypothesis never achieved.
A better candidate example might be string theory. It has achieved tremendous influence without a bit of direct evidence, and it's more zealous practitioners are famous for their persecution of doubters. Neither of those things is evidence that the string hypothesis is wrong - but it's equally certain that it is an unproven hypothesis. Of course it can't be compared in practical importance to any of the other hypotheses. If string theory is true and useful, we will likely find some evidence for it eventually, but it's practical importance will be confined to some faculty appointments, at least in the medium term. Meanwhile all the others concerned directly affect the lives and health or millions or billions.