While Bargh's reply does mention conflict of interest, it also mentions significant methodological differences..
It does look that both replications didn't replicate the relatively small number of primes in the priming material. Bargh has a consistent explanation with links to other studies why it is important.
This is interesting, if only because the study in question is one of the more famous examples of priming effects - it's the one I tend to use when I introduce people to the idea of priming. (Ironically, the failed replication study also mentions a further experimental manipulation that does show priming effects - affecting the experimenters rather than the subjects.) Bargh's reply is also unusual in that it focuses significantly on extra-scientific arguments, such as attacks on the open access business model of PLoS ONE.
I was instantly reminded of The Golem, which "debunks the view that scientific knowledge is a straightforward outcome of competent theorization, observation, and experimentation". The examples on relativity and solar neutrinos are particularly engaging - it's not just psychology where experimentation is problematic, but all of science.
The linked blog also contributes useful observations of its own, such as the "rhetorical function" of the additional experiment in Doyen's study, how online publication makes a difference in how easily experimental setups can be replicated, or a subtle point about our favorite villain, p-values.
EDIT: added link to source. Heartfelt thanks to the two readers who upvoted the version without the link. :)