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.
Agree to this. Though this is how I perceive the Legendaries Genders. (some will be repeated)
I. either Male / Female (due to sprite color/aesthetics)
Mew, Celebi, Jirachi, Manaphy, Shaymin (both formes), Victini, Uxie, Azelf, Phione, Suicune, Heatran, Arceus
II. Mostly feminine
Cresselia, Shaymin (both formes), Latias, Kyogre, Mesprit, Meloetta, Reshiram, Mew, Celebi, Phione, Suicune, Arceus
III. Mostly Masculine
Articuno, Zapdos, Moltres, Mewtwo, Entei, Raikou, Latios, Groudon, Rayquaza, Deoxys, Dialga, Palkia, Giratina, Darkrai, Cobalion, Terrakion, Virizion, Keldeo, Zekrom, Kyurem, Jirachi, Manaphy, Victini, Uxie, Azelf, Heatran