It's actually very refreshing to see someone from the male half of the species asking this question and requesting opinions. From a feminist standpoint, I've long considered PZ to be an ally to the cause (and a feminist himself) so he hasn't disappointed me here.
I already voiced my opinion in the comments, but since this is my blog and I can say whatever the hell I want, I'm going to repeat myself here and expand it a bit.
So, how can we get more women involved in atheism and/or skepticism? I'm looking at this from more the viewpoint of skepticism, mostly because I don't even have a passing handshake with organized atheism.
Oh noes, not affirmative action! What the fuck ever. I don't think all women are shrinking violets that would shy away from attending a giant sausage fest of events. I've gone to a great many events (for various organizations) where women were very much in the minority. But I also know that I was not entirely comfortable in doing so - and would often seek out other women if my discomfort level got out of control - and this even though I don't have a problem being confrontational and I'm reasonably intimidating when I want to be. The more women you have at your event, the more welcome other women will generally feel there. And the way you advertise your event as a safe and interesting place for (feminist) women is by having having female speakers - or in a pinch, outspoken male allies. So go out of your way to find more woman.
I think the dearth of female speakers/presenters at events may be produced by a sort of negative feedback loop. Women are sometimes treated as if we don't have anything interesting to say, therefore we are not given opportunities to speak, therefore anything interesting we might have to say is not heard by a broader audience. There aren't many women who are "big names" within the skeptical movement, compared to men. A lot of that fame within the movement feeds on itself. If you've got a little fame as a skeptic, you get asked to speak at an event, and thus you are more famous and get asked to more events. Unless you're given a platform to pontificate upon, it doesn't matter how interesting and erudite you are. You won't be heard.
Someone in PZ's comments pointed out that there's plenty of female attendance at woo events. I'd lay good money that those sort of events are strongly aimed at women, because it's very socially acceptable for women to be into all sorts of unscientific shit. Encourage women to shy away from the hard rationalism of science and then give them somewhere that their socially acceptable "intuition" can have free reign and be praised, you're damn right they're going to feel comfortable and happy going to those kind of events. So what can we do about that? Prominently advertise the women who are involved in skepticism and do our part to making rationality and intellect laudable female traits. Continue the general work of science cheerleading and promotion of skepticism, but make certain that women are involved in that as well. Promoting skepticism with an all (or almost all) male face unfortunately just contributes to the image that skepticism is male territory and women have no place there.
We have varying degrees of comfort about sexist jokes. Personally, I know I am completely unbothered at times, and at other times I'm as offended as hell. Not all women are like me. Some are more sensitive or less sensitive. But if you foster an environment where it's okay to make sexist comments or jokes, and the only male reaction to it is either laughter or a dismissal of female complaints, you can't really blame some of the women for just checking out entirely. This even comes down to individual responsibility of attendees. If you want to see more women at conferences, then when one of your fellow men gets creepy at some poor woman whose only mistake was being in his presence while in possession of breasts, you'd damnwell better tell him to knock it the hell off. If you really want more women at these events, then you'd better want us there for our contributions, and not just because you want someone that you can hit on.
Enough with mansplaining. Seriously. And the next person to claim that my pitiful ladybrain just can't handle math is getting punched in the face. I mean it.
There are probably other barriers to female attendance. If you look for the comments on PZ's post from someone with the nick Cerberus, she makes some really good points as well - like how often libertarianism is given a free ride, and how that may really put some people off. (I tend to tune out the libertarian stuff, since I am so, so very done with it.) The big thing is that there are barriers, and acknowledging them is the first step to taking them down.
And is this a problem that actually does need to be addressed? If we're just in this for show and to pat ourselves on the back, well, in that case it's fine to dismiss the potential contributions of a great many people because getting them involved is too much effort. If we're just in this so we can feel superior to all those poor schmucks who just aren't rational enough, then it's a nice ego boost to shake our heads and cluck our tongues about all those sad women, who just can't do skepticism because they're wired to be "intuitive" and "feeling," whatever the fuck that means.
If we're serious about our cause and our mission, however, then we've already waited too long. It's a problem and a sad waste that we're missing out on so many people that could otherwise be contributing. It's a problem and a base hypocrisy that some are not casting a skeptical eye at our own social institutions. And it's long past time things changed.