David Zetland:
Last week, I sent this email (edited for anonymity):
I hereby resign my position on the advisory council of the Journal of X.
I do this because X published a paper I refereed, a paper that I considered unsuitable for publication in a peer-reviewed journal.
I know that it's awkward to tell a guest editor that they need to fix their paper, but we academics should not let power or authority get in the way of open, critical and honest scientific debates. I was disappointed that the author/editors did not seem to take my criticisms seriously. Even worse, they did not even bother to respond to my concerns (as is normal in the review process) before proceeding to publication.
I do not want to participate in an endeavor that produces results like this.
The worst part is that the author is likely to claim the paper as a "peer reviewed article" in their CV and for promotional purposes. Will their supervisors know that the paper wasn't exactly peer reviewed? Will the citizens paying their salary know that their "scientific contribution" is flawed?
The very worst part of being a referee (other than reading bad and/or long papers) is when the editor (or in this case the author/editor?) decides to ignore your opinion and, probably, suggestions for improving the paper.