There is an interesting post over at Drug Monkey on the issue of bias in peer review. I think that there are two issues that really strike me as important in peer review and it is easy to confuse them. One is the idea that individual reviewers will have preferences for the types of research that they like to see done. This issue is difficult, if not impossible, to solve.
Two, and more annoying, is the issue of competence and coherence in review. I cannot enumerate the number of reviews that I have gotten that had questionable elements. I remember one journal claiming that they could not publish a paper that had an "unverifiable assumption" in it. The assumption in question, no unmeasured confounders, was a pretty standard assumption for all research. Even clinical trials have this issue with loss to follow-up not necessarily being at random.
But the reviewer is protected from strong complaints of "what were you thinking?". Now, I too have certainly done peer reviews that could have been better. I think we all can think of examples of this. So I am not claiming to be "special" and I am sure that I have been cursed by an author more than once for not "getting it".
But I think that these concerns are what gives anonymous peer review it's bad name.