Seeding and switching trials—Sometimes companies will conduct trials simply to get doctors to prescribe their drug. These "seeding trials" are often scientifically meaningless. They have no clear question and no controls. But they are conducted on a large scale, and "investigators" (often ordinary doctors, not researchers) are paid substantial sums to enter patients into the trial. A variant is a "switching trial" in which a doctor is paid to switch patients from their usual treatment to the new treatment. These sorts of trials will rarely make it into major journals, but many may be published somewhere—and then used to promote the drug with doctors, most of whom are scientifically naive.
Postmarketing surveillance—Yet another variant—with perhaps more scientific justification—is postmarketing surveillance. Many adverse effects of drugs do not emerge until after they are on the market, so it makes scientific sense to gather data on patients taking new drugs, but it can also make marketing sense as a way of getting doctors to prescribe the drug. Again doctors may be paid substantial sums "for expenses." My guess is that they rarely explain this to patients. Instead, patients may be flattered to think that they are getting the newest (with a false implication of best) treatment. These trials will often be published, sometimes in major journals—because they give important data on adverse effects.
Placebo controlled trials—Pharmaceutical companies are usually required to conduct a trial of their new drug against a placebo to get a licence for the drug. This requirement may conflict with the Declaration of Helsinki, which deems it unethical to give patients a placebo if an evidence based treatment is available. As most new drugs are not completely new but "me toos," this conflict arises often. What patients and doctors want to know is whether the new drug is better than existing treatments. But pharmaceutical companies have a horror of "head to head" trials, where treatments are tested against each other in trials that are big enough to give a clear answer. A clear but unfavourable answer would be dreadful for a company that had spent hundreds of millions of dollars bringing the drug to market and tens of millions on trials.
DeAngelis, Smith, Angell, who's next? The list of medical journal editors who are noticing that something smells fishy is growing...