Every faction, in all the sciences, have their own journal. As a scientist, your goal is to get published - so you submit to the journal with the editors that are most likely to approve your article. You then become associated closely with that journal and then become invited to peer-review other articles for inclusion in that same journal.
Inevitably that means that the cycle continues and journals develop a reputation for a certain point of view on specific issues, similar to newspapers developing a certain political affiliation.
The peer-review process is not perfect, but like democracy, its the best system we've got.
"Climate debate aside, we need to invent news ways to do review of papers and grants that is not totally dependent on self-policing of scientists. Any suggestions?"
Aside from your gross generalization of "scientists" as a class of people, who else could you possibly suggest to understand and evaluate SCIENTIFIC proposals and SCIENTIFIC papers besides SCIENTISTS?
In any case, in the specific case of climate science, it is true that "skeptic" papers very rarely get published in respected scientific journals. This is not, however, due to some vast conspiracy where "some rejected should not have been" - it is because the science is truly bad in most of these papers.
Besides, being published in a journal does not make it the truth - if someone truly believes in their research they are free to disseminate it in other ways, especially in "the internet age".
As for the famous quote "even if I have to redefine what peer-review literature is" - just because he is a scientist doesn't mean everything he writes has to be taken literally. He is annoyed, privately I might add, at people pushing what he views as bad science and is simply voicing his opinion. There is no evidence that any papers were actually excluded, and there are a few decent "skeptic" papers cited in the IPCC report referenced in the emails. There is no censorship going on.
There is far more money available on the "denialist" side - than from publicly funded climate research, especially in today's economic climate when governments are trillions in debt and the public opinion of science in general is a confused mess.