Wikileaks revealed that the NYT was in coordination with HRC's campaign to publish flattering stories. I think the credibility of the news organization is over.
edit: I can't think of a good reason to downvote this question (please do explain), but I'll rephrase: the Judith Miller Iraq reporting was bad to say the least, and they got rid of her. In this case I am under the impression that the problem is a few isolated cases, but I'm not well educated and am possibly missing something. What about these emails makes this a sweeping issue over the whole organization, as opposed to a few reporters having abused their welcome?
I still cannot believe this. In fact, it's probably the single most poignant fact of the Iraq war. It shows us that the NYT was not outraged by the "mistake" but supported what was effectively a propaganda effort.
This is why I liken the NYT to America's Pravda. The stories it runs help to bolster the legitimacy of certain institutions and create PR and misdirection as needed to allow the status quo to continue.