I just found out about BioMed Critical Commentary. Here’s an excerpt from the site’s philosophy statement.
The current system of scientific journals serves well certain constituencies: the advertisers, the journals themselves, and the authors. It is the underlying philosophy of BioMed Critical Commentary to serve the readers in preference to any other constituency.
In particular, this site could serve as a public forum for criticism that journals are not eager to publish. It could be a good place to discuss specific examples of irreproducible analyses.
This is an interesting idea—it seems it might make more sense if it could be integrated with journal web sites themselves so you wouldn’t have to go to a separate web site to comment.
Actually it is better not to be at a journal, since no matter what the topic, there would be a single place to go and oftentimes commentary may relate to multiple publications at different journals.