There's a lot of pseudoscientific or grossly biased "studies" out there that pretend to be actually doing real science. That really can't be stopped. Lots of organizations spend a lot of money to come up with "evidence" to back up whatever they like to promote. What upsets me is when these "studies" get published under the guise of actual scientific work. Some of theme are even peer reviewed. The great PZ brought up an example today from the Southern Medical Journal of a study that showed that prayer improves vision by recruiting subjects from a church revival, not blinding and not having a control. If the Southern Medical Journal is a legitimate medical journal, how did this study make it past the editor (let alone through peer review)? Clearly, the scientific process doesn't matter for this journal.
There are a lot of science journals that have been publishing pure crap (I suppose in order to get more readers) and it really diminishes their value. Not quite this bad, but even bigger named journals like the New England Journal of Medicine have been trending towards legitimizing pseudoscience, such as this recent review of acupuncture (discussed by Orac). A few years ago, I actually got in an argument with an editor from the American Journal of Health-System Pharmacy because they published a letter to the editor that used a posting from prolifeblogs.com to support their argument against the availability of over-the-counter emergency contraception. The response I received from the editor was that they can't be selective against the literature their contributors cite (yes you can! And, a blog post can't count as scientific literature).
So, similar to my post on companies that underhandedly promote religion, I want this post to include a (probably) growing list of scientific journals that aren't exactly scientific:
Journal of Cosmology
The Open Information Science Journal - accepted a fake paper without review from a couple of people from MIT claiming to be researchers at the "Center for Research in Applied Phrenology" (CRAP) - as long as they sent an $800 check to an address in a tax-free zone in the UAE.
Has Ulterior Motive:
Australasian Journal of Bone and Joint Medicine (sham journal for Merck provided by the supervillain of scientific journals: Elsevier).
The Journal of Global Drug Policy and Practice - funded by the Department of Justice and only publishes "research" that shows that punishing people is the only way to reduce drug use.
Ignores scientific process for publicity/money/religion:
An exhaustive list of preditory open-source journals can be found at Scholarly Open Access
American Journal of Health-Systems Pharmacy
American Journal of Surgery
British Journal of Psychiatry
Journal of Medical Hypotheses
Social Science Research
Southern Medical Journal
... and more coming when I get the chance to get to them.