Well, they always say better late than never, right? I promised to answer the questions posed by Mein Hermitage's Q&A sans babies, so here it goes:
1. How do you command the attention and respect of men in academic settings (e.g. classroom, conferences, faculty meetings)?
In my experience with colleagues, the most important thing is to be good at your job, be professional at all times, and don't lose your temper over the small stuff (even if it is really hard). Especially when you are starting out, you don't want to be known as "THAT woman, you know the one who is touchy and has no sense of humor". For everyone, and especially for visibly obvious members of underrepresented groups, it is your science that people will pay attention to. Without a strong base of good science/other work, no one will care what you think and that goes double for women.
In the classroom, it is REALLY important to establish yourself as in charge. When my large undergrad class gets too loud, I just stop speaking. If it continues for more than 30 seconds or so after that, I remind the class that they need to know the material on the exam whether we cover it in class or not. At that point, usually disruptive students will be shushed by their peers. If there are students who repeatedly question your authority publicly and disruptively, throw them out of the class. I've only had to do that once (when I was a TA), but it really works to establish who is in charge. This is the nuclear option--only use it as a last resort. Never, ever BS something if you don't know the answer. Your students will definitely respect you more if you say you don't know, but you will look it up and let them know next class (and then DO THAT!). in my experience, most students will respect you if you show up to class prepared, show an interest in their learning, respond to questions in some manner, and show some enthusiasm in the classroom.
2. How should women dealing with a two body problem handle assumptions that their career is secondary to their partner's?
I didn't have a two body problem in that my partner is not in research. We did have to make sure my partner could find work wherever I ended up, and I did give my partner veto power over our final location (after all, we both have to live there!). That said, I would ignore your peers' opinion on this. Your advisor will (hopefully) know your career is primary. When it came up interviews (and it almost always will, legal or not), I just said that my partner is not in academia and has lots of job flexibility and left it at that. At ProdigalU, I've seen searches with both male and female trailing partners, and in neither type of situation did the partner situation come up in post-interview discussions of the candidate.
3. What would you like to see from tenure-track and not-yet-tenured menfolk? How can they pitch in?
In my opinion, the most useful thing that concerned menfolk can do are to call out people who are acting like sexist asshats, even if no women are present. Letting the lab degenerate into a frat house party when they women are not around makes it clear that science is a boys club that women can sometimes visit. Speaking up about an inclusive environment is sometimes easier for men, because they are not going to be accused of "looking for sexism" or being "a humorless bitch" for saying something about nasty jokes or comments.
Another thing that men can do is to make sure they nominate/suggest kickass science women as well as kickass science men for awards and seminars. If only male speakers come to mind at first, think a little harder about women active in your field doing interesting science. It is a habit that will break with practice--I noticed the same thing in my own suggestions for speakers (they were overwhelmingly male) until I started thinking more deeply about some of the papers I'd recently read/talks I'd attended given by women doing great stuff.
Don't single people out because they are women. I want to be treated like any other scientist. I just don't want to be the only one thinking I belong in the room.
4. How do you deal with insinuations that you were only chosen for a position/award/etc because of affirmative action?
I ignore them. Most of the people who say these things are jealous or insecure. There is nothing you can say to change their minds, so don't bother.
I can say that although I have experienced individual acts of sexism, and faced discriminatory environments, most of the people I have met in my career are just people trying to get ahead and also be a decent human being. If you act like you are self-confident (even if you feel like an impostor), know your stuff, and work hard, that will take you a long way.