One angle I wish Saletan's article had touched on, and which might go part way towards explaining the persistence of a "male homosexual gene" (if such a thing exists), is the possibility that such a gene may confer high indirect fitness benefits on the carrier of such a gene. Presumably gay men in traditional societies would be less likely to have children and thus pass on their genes; however, childless homosexual men would have more time and energy to offer protection, teaching, and attention to the children of close relatives, who also share many of the gay man's genes. This may help explain why the androphilic effect that Saletan speaks of seems to operate through the gay man's relatives on his mother's side but not on his father's side:humans, like many species, engage in "extra-pair bonding," meaning that one's close genetic relationship is only certain when the relation is through the mother's side. Indirect fitness seems to be a powerful actor in many species and there's no reason to think it doesn't apply to human behavior.

Good point, and I think other theories have touched on this - according to evolutionary theory, this provides a survival benefit to the children, as well as enable the homosexual relative to see to it that their genes (via their nephews and nieces) survive and perpetuate.

Here's another one: there could be several genes that contribute a little bit to gayness, so that on average, a person will have one or two gay genes and be slightly gay. This was beneficial during our evolutionary past because men would often decide who their daughters would marry. If the guy had no gay in him, he would marry his daughter off to an ugly ass, and his grandchildren would be undoable. Meanwhile, I would marry my daughter to Daniel Craig's physique in that Bond movie.

Sometimes though, a person will end up with all of the gay genes flipped on and he'll run around in short shorts screaming "Oh my God...Look at all these men!!"

You could test this by looking at adopted kids in the US with racial heritages from various cultures. See if the cultures that traditionally had man on man selection have more gay offspring. If you think about it, Indian men sound kind of gay.