It's clear that the incentives for journals are terrible. We should be looking to fix this. We seem to have a Goodhart's Law problem, where credibility is measured in citations, but refutations count in the wrong direction. Right now, there are a bunch of web sites that collect abstracts and metadata about citations, but none of them include commenting, voting, or any sort of explicit reputation system. As a result, discussions about papers ends up on blogs like this one, where academics are unlikely to ever see them.
Suppose we make an abstracts-and-metadata archive, along the lines of CiteSeer, but with comments and voting. This would give credibility scores, similar to impact ratings, but also accounting for votes. The reputation system could be refined somewhat beyond that (track author credibility by field and use it to weight votes, collect metadata about what's a replication or refutation, etc.)
Related to: Parapsychology: the control group for science, Dealing with the high quantity of scientific error in medicine
Some of you may remember past Less Wrong discussion of the Daryl Bem study, which claimed to show precognition, and was published with much controversy in a top psychology journal, JPSP. The editors and reviewers explained their decision by saying that the paper was clearly written and used standard experimental and statistical methods so that their disbelief in it (driven by physics, the failure to show psi in the past, etc) was not appropriate grounds for rejection.
Because of all the attention received by the paper (unlike similar claims published in parapsychology journals) it elicited a fair amount of both critical review and attempted replication. Critics pointed out that the hypotheses were selected and switched around 'on the fly' during Bem's experiments, with the effect sizes declining with sample size (a strong signal of data mining). More importantly, Richard Wiseman established a registry for advance announcement of new Bem replication attempts.
A replication registry guards against publication bias, and at least 5 attempts were registered. As far as I can tell, at the time of this post the subsequent replications have, unsurprisingly, failed to replicate Bem's results.1 However, JPSP and the other high-end psychology journals refused to publish the results, citing standing policies of not publishing straight replications.
From the journals' point of view, this (common) policy makes sense: bold new claims will tend to be cited more and raise journal status (which depends on citations per article), even though this means most of the 'discoveries' they publish will be false despite their p-values. However, this means that overall the journals are giving career incentives for scientists to massage and mine their data for bogus results, but not to challenge bogus results by others. Alas.
1 A purported "successful replication" by a pro-psi researcher in Vienna turns out to be nothing of the kind. Rather, it is a study conducted in 2006 and retitled to take advantage of the attention on Bem's article, selectively pulled from the file drawer.
ETA: The wikipedia article on Daryl Bem makes an unsourced claim that one of the registered studies has replicated Bem.
ETA2: Samuel Moulton, who formerly worked with Bem, mentions an unpublished (no further details) failed replication of Bem's results conducted before Bem submitted his article (the failed replication was not mentioned in the article).
ETA3: There is mention of a variety of attempted replications at this blog post, with 6 failed replications, and 1 successful replication from a pro-psi researcher (not available online). It is based on this ($) New Scientist article.
ETA4: This large study performs an almost straight replication of Bem (same methods, same statistical tests, etc) and finds the effect vanishes.
ETA5: Apparently, the mentioned replication was again submitted to the British Journal of Psychology: