Actually the first pregnant male Star Trek story I read was a fan fic from before 2003 entitled "What" by Susan DeFluke (she is legendary in Voyager fic circles).
There are tons of pregnant male stories out them (none of them sexy) usually involving Paris and Chakotay in one of those utterly OOC (and, as mentioned, totally unsexy) stories where one turns into a simpering submissive.
I'm with you, Teacake, on the "don't breed with Chakotay" thing. The J/Cers out there are already going flaky over the book; that would be the death knell for rational Trek board postings for weeks.
But as for breed Janeway with whom? My question -- why breed with anyone? Some women are allowed to just have a career, you know. That said, if I see Janeway with anyone it'd have to be Picard. Equals, and all that. Plus there'd be the dinner conversations -- "remember our days in the Collective?" or "Which Quadrant of the universe do you prefer, or are you more into timeline divergences?" or "What was YOUR favourite alien possession, hun?" ... the possibilities are endless.