I've offered my opinion in the comments on various blogs, so I'll just resummarize it here -- this time with pictures!
On the issue itself, I fall in the so-called "New Atheist" camp, in the sense that I do not think religion and science are compatible1, and I don't think there is some sort of social responsibility and/or critical pragmatic imperative that ought to prevent me from saying so. Others have expounded on this position at great lengths, so I won't bother to rehash any of that.
Perhaps the more unique take I have on it is that I think that, strategically, it is important that we have both "New Atheists" and accomodationists -- and maybe even desirable that the accomodationists distance themselves from us, though certainly not as loudly or as shrilly as Mooneybaum feel compelled to do.
Modern atheists often draw an analogy to the gay rights movement, and while we certainly do not face the level of discrimination that gay people did and still do (the state of NY has never barred Atheist Marriage, AFAIK...), I think there are a number of areas where the analogy is apt. Certainly the Out Campaign is an idea I support, as you can see a few hundred pixels to your right.
So, even though I disagree with the NCSE's position on accomodationism, I am secretly glad that they do it. It probably is strategically desirable, but only if at the same time you have us vocal atheists saying, "Uh, no that's not quite right." If the accomodationist position were the only active one, it would be a strategic dud, because the other side would always be paddling harder.
I think the accomodationists and the "New Atheists" actually compliment each other quite well. As entertaining as this little blogowar is (and now you can buy the book! When is the movie coming out, Mooney?), I really hope it just kinda quietly goes away. It doesn't do anybody any favors. Well, except me, because I indirectly managed to get a lot of blog hits from it, but I don't think that was Mooney's or Coyne's original intention...
1That is, I think religion as most people understand it is logically contradictory to science -- not that a reasonable person couldn't believe both... I think I'm a reasonable person, and I believe a number of irrational things, e.g. that my wife and I were meant to be together, that my son is the smartest four-month-old on the planet, that anybody will still be interested in my blog after next week... The differences are 1) I know these beliefs are irrational, 2) I don't try to convince anybody else of my own personal irrationalities, and 3) I don't pretend they are compatible with a scientific worldview, so that if it eventually becomes undesirable or dangerous to continue to hold these irrational beliefs I will have no trouble discarding them. In fact, if theists would apply those three criteria to their beliefs, I don't think there'd be much of a role for the so-called "New Atheists", because what would we have to complain about?