Well, the News is abuzz with discussion of a controversy involving lung cancer studies that were funded by tobacco associated money (e.g., see MSNBC and TIME and the NY Times). The issue is that apparently the source of the money was hidden through some sort of laundering of the money through a foundation.
As many readers know, I am a bit obsessed with open access to scientific research publications. This here is a case where the need for openness goes well beyond publications. Here there is a need for openness about funding and conflicts of interest and the roles of all participants. In this case, I am not sure what could have been done by the journals involved to vet the funding of the project more carefully. But nevertheless, science in general can be severely hurt whenever there are cases of even the appearance of conflict of interest. I do believe that open access journals help in this in that anyone, anywhere, can look at the publication as well as the descriptions of the funding sources and the authors contributions. The more eyes we have on research products, the more likely problems will be discovered and (possibly) the less likely it will be to happen again.