Homosexual probably within a few decades (within the half century, perhaps). Can't speak for if it'll be one of those "I'm gay and proud of it" sort of things that's very public in the election, if it'll come up but go unnoticed (hey, maybe times will change that much), or if it just won't come up/the president won't come out about it.
Atheist, dunno. Maybe a similar timeframe, as atheism is growing in the States, and is now a significant minority. Agnostic may be more likely, since the term "atheist" has been given negative connotations by the religious right.
Woman president, I see no reason why that couldn't happen in 2016. I don't think the country in general would have a problem electing a woman to the office of president. Though frankly if they do (on the basis of "she's a woman") they should lose their right to vote.
I'd be curious to see how long it takes before we get a Muslim president, personally. Or a Native American--that would certainly be a biggie. I don't know that we'll ever have a Muslim president, just because the political/social climate will probably stay about as it is for a long time and there will be a general stigma against it. Native American, I think it's just a matter of finding one to run--there aren't a whole lot of Native Americans in politics, much less in the executive branch--but I don't think there would be any problems with people not wanting to vote for them.