I keep in mind the anime =/= game rule. So for genderless Pokémon like Legendaries, I just go by what I think they look like. I consider Mew to be pretty girly, but it's very possible the Mew from the eighth movie is an entirely different Mew--even then, I consider the Mew we know as a female. I believe Darkrai is a male (the voice helps), just like Dialga and Palkia are both male as well as Giratina. I also think Celebi is a male (unless there are actually more than one Celebi out there, the fourth movie screwed that up with the ending), as well as Jirachi, and a few others. Yeah, I think there are more male Legendaries than there are female for some reason.
As for the normal genderless Pokémon, chances are majority of them are genderless, but as they're odd-looking Pokémon, the humans probably haven't been able to figure out where the sex organs are on them--if they have any to begin with. I'm not even sure if they do lay eggs to begin with, but as there are a bunch of them running around, they probably do breed. Thus this whole entire paragraph got contradicted left and right.
So it's more-or-less an opinionated question, since the franchise is never going to answer this.