There's been longstanding debate over the way in which manuscripts are handled by the EGU/Copernicus journals. The current system is that publication fees are charged for submitted manuscripts, which are professionally typeset (hence incurring significant costs) and appear in an on-line “Discussion Journal” like CPD, GMDD etc where they remain as part of the public record (with DOI etc) irrespective of whether a final peer-reviewed paper appears or not in the non-D journal. There are several drawbacks with this approach, though its originators and advocates have always argued that the benefits outweigh these.
Well, it's all changing now anyway. From January, submitted manuscripts will not be professionally typeset, the Discussion journal will cease to exist (though the submitted manuscripts will still be public and citeable), and paper charges will only be applied after the paper has been through peer-review. It will be interesting to see how this affects the journals, and whether for better or worse. As for me, I'm pretty ambivalent about it. Paying charges in advance was always a bit awkward and puts editors in a difficult position when rejecting papers (at GMD, the unofficial policy was to offer a hefty discount on fees for their next submission). On the other hand, perhaps it does dissuade a certain amount of dross - though it apparently didn't help with this nonsense. Anyway, the new system will be much closer to the standard model for journal publication, while retaining the special feature that not only the final manuscript, but also the review process, is on-line and open to all.