In HOOKED, I spent relatively little space discussing pharmaceutical ads in medical journals. I did this in part because I figured that ads are less worrisome as a source of influence over physicians, due to the fact that they are very clearly labeled as "ads" and no one tries to pretend that they are education, etc.--unlike other practices such as continuing education, visits from drug detail people, etc. Had I seen a paper that appeared last summer, I might have devoted more attention to the issue.
Fugh-Berman and colleagues (writing in PLoS Medicine, an internet journal that accepts no advertising) dug deeper than I had, especially in spotlighting the ways that medical journals go fishing for ad business. They had the good sense to check out some of the medical journals' own websites in which the abjectly plead for advertising revenue, putting forward an image that is pretty far removed from their "public" image as dispasionate, incorruptable purveyors of scientific truth. The authors conclude that the near-total reliance of the journals on ad revenue from the pharmaceutical industry cannot help but bias the editorial decisions. They make the interesting suggestion that it has long been thought "professional" that top-notch journals only advertise pharmaceuticals and things that are part of direct service to patients; they do not run ads for cars, or things that have to do with the physician's own lifestyle. Fugh-Berman et al argue that this "professionalism" actually undermines professional values in medicine and that if the advertising in medical journals was more diversified, it would at least be a help.
Fugh-Berman A, Alladin K, Chow J. Advertising in medical journals: should current practices change? PLoS Med 3:e130, 2006. http://medicine.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pmed.0030130