The Hansen paper (submitted manuscript!) has provoked me into mentioning that the EGU are in the process of revamping the discussion phase of their on-line open access publications. There have been a number of complaints over the years that the open publication of the pre-review manuscript can be confusing, as it may lead people to think that these are peer-reviewed publications (which they are not). I've never been particularly convinced by this, and you only have to look at the process to see what is going on, but then again, if people are going to be confused, maybe it is reasonable to wonder if the process could be clarified. A “watermark” on the title page was already added a few years ago, and they have also recently improved the way that the website links and indexes the manuscripts - pointing more clearly to the final paper when available, so people do not read and cite the original version unless they specifically want to.
I'm not sure quite how finalised the new plans are, but at the time of the last EGU meeting one of the proposals was that the authors' own typset manuscript (eg a fairly plain LaTeX template) would be posted up as-is rather than being formatted into the in-house EGU online style. I don't really like the EGU style so that's already an improvement from my perspective. Another potential benefit is that this would eliminate one source of up-front cost which may pave the way for normalising the publiction fee model to a pay-on-(peer-reviewed)-publication model rather than pay-on-submission. There are arguments on both sides of this - pay on submission may reduce the number of poor submissions, but it can be administratively difficult and may lead to both a presumption of acceptance and hard feelings when a paper is rejected.
Ultimately, I don't think these changes will have much effect on the rare cases where people deliberately publicise their submitted manuscrips, as Hansen appears to have done. Most journalists won't understand, or care about, the details of the peer-review process. Nevertheless, I don't have much sympathy for Ken Caldeira's claim that publishing the review process is a form of “pollution” of the peer reviewed literature. No-one sane would routinely read the discussion phase of the journal, and the point behind the publication of these manuscripts is not to double the amount of material that scientists are supposed to read, but to give people the chance both to look at how a particular paper passed through the peer-review process, or to comment on a manuscript that is particularly noteworthy. To that end, I'm happy to see that the Hansen manuscript is well on its way to being the most heavily-commented paper on ACPD, though predictably most of the comments seem to be from crazies. At least they are thereby distracted from commenting on my blog :-)