Oo, I had a thread just like this a while back. I'll answer it all again and add a little explanation for each. Little note: I don't always associate sleekness and grace with feminine Pokemon or strength and burliness with masculine Pokemon.
Articuno: F
Moltres: F
Zapdos: M
MewTwo: M
Mew: F
Articuno and Moltres strike me as very feminine. Moltres has dazzling fire on its head and wings, and its triangular beak and eyes yet rounded body suggest female qualities. It could easily be male, however. I associate Ice with femininity, but also Articuno just looks like something so stern yet so understanding. Zapdos is jagged all over and looks tough-as-nails mean, so I'd call it a boy. The birds can really go either way, though. MewTwo is male for me because... well, it has a male-looking stature. Also, Dan Greene's voice is forever imprinted in my mind for MewTwo. Mew represents an embryo, and all embryos (at least for humans) start as females. It's also pink and looks like an adorable little cat, so there's that.
----------------------------------------------------------------------------------
Entei: M
Raikou: M
Suicune: F
Celebi: F
Ho-Oh: F
Lugia: M
Entei's ruffled mane and thick stature are very masculine to me. It takes very much after a male lion. I'm also influenced by the movie, in which Entei is some sort of incarnation of the little girl's father. Raikou may be sleek and speedy, but it's facial structure strikes me as male. Raikou is kind of the in-between here, as I could essentially see it going both ways. This is because it seems to be more naturalistic-looking, and while people confuse Entei for either a dog or a lion or Suicune for a cheetah, leopard, or wolf, everyone always associates a tiger with Raikou. Suicune can be nothing other than female because it's the epitome of grace and beauty, and the most beautiful Pokemon ever created in my eyes (even though Entei is my favorite). It has tiny feet, a flowing purple mane, a thin frame, and represents feminine elements such as wind, water, and purity.
And now for Celebi, the little onion fairy. It's another one of those ones that could go either way. But it has a lot of black around its eyes, suggesting eyeliner, and its cute and friendly demeanor definitely seem girlish. Ho-Oh just looks very feminine to me and it's hard to explain why, but I'll try. It seems like it would be so incredibly powerful yet its mysterious, beautiful, and kind of motherly-looking even... that may be because female birds (as well as their male partners) actually care for their offspring. Lugia is big and bulky, that's really the only reason I see it as male. That, and there's a saying that goes, "Mother Earth and Father Sea" or something like that. It could go either way, though.
----------------------------------------------------------------------------------
Registeel: N/A
Regirock: N/A
Regice: N/A
Jirachi: M
Deoxys: N/A or M
Rayquaza: F
Kyogre: F
Groudon: M
The Regis are perfectly robotic and therefore have no gender to me, no matter what. I see Jirachi as a male for no particular reason at all. Deoxys, I was going to say N/A, but since its eyes look sentient instead of machine-like I'll also classify it as male. It's figure just suggests it, and robotic-looking things tend to strike me as male (unless they don't take after a humanistic figure, like the regis). Rayquaza is female because it's associated with the sky and anything serpentine I usually associate as female. Kyogre represents water, which is typically considered a feminine element, and it is based off of a whale, which, in the case of the orca, is matriarchal. Otherwise whales are looked at as beautiful, gentle creatures that are still incredibly strong. Groudon is hard and brutish-looking, and is associated with earth and fire. It looks angry and unforgiving, thus giving it a more masculine appearance.
----------------------------------------------------------------------------------
Uxie: M
Mesprit: F
Azelf: M
Darkrai: M
Manaphy: M
Phione: M/F
Shaymin: F
Regigigas: N/A
Dialga: M
Palkia: M
Giratina: F
Arceus: F
I never cared about the Lake Trio and I tend to forget they exist. It was tough deciding Uxie's gender, but I decided it and Azelf are male, and Mesprit female, because of their depictions in Mystery Dungeon. Darkrai looks kind of a like a ballerina with those long legs, but it also reminds me of those whiny emo boys I used to see in school, so yeah. Manaphy looks like a future prince, something that's cute and small now but will grow up to be stern and kingly. There are many, many Phione in the ocean, right? So both genders for them. Shaymin is fluffy-wuffly and wears a flower in its hair, so I definitely see it as girl. In its Sky Forme it's just a tomboyish girl. Regigigas is self-explanatory. Now Dialga is blue and Palkia is pink, but I see them both as male for no particular reason. They look kind of insentient and primordial, like they're just creatures driven by instinct and nothing else, and they're dinosaurs which are inherently masculine. Giratina has "tina" in its name, and that's honestly some of the reason it seems feminine. It converts into a snake-like Origin Form. Yep, snakes are chicks to me! Arceus should probably be both genders, being the God of Pokemon and all, but the flowing wisp of... whatever that is on its head looks like hair, and plus... is it just me or does it look pregnant? The part of its belly with the hoop around it is puffed out and bulging.
----------------------------------------------------------------------------------
Terrakion: M
Coballion: M
Virizion: F
Keldeo: M
Victini: M
Genesect: N/A
Reshiram: M
Zekrom: M
Kyurem: F
I don't care enough about the Quintuplets to go into great detail about them... Terrakion looks like it has the strength of a bulldozer and Coballion has horns like a male antelope. Virizion... well, just look at it. Keldeo is a masculine My Little Pony doll. Victini was a tough choice, but ultimately it seems like a mischievous little boy who looks a little girly. I can't really explain that one well, sorry. Genesect is, of course, very machine like so it gets no gender.
Reshiram, although many see it as feminine, actually just seems like a very proper, graceful and royal-looking male. Have you ever seen Howl's Moving Castle? This is a weird comparison, but Reshiram is kind of like the Howl of Pokemon... it has tons of feminine qualities but it just screams "MALE!" Zekrom, my favorite legendary besides the Legendary Beasts, looks incredibly muscular and has Zeus-like powers, thus, male. Kyurem represents Ice, and is therefore female.
----------------------------------------------------------------------------------
Xerneas: M
Yveltal: F
Zygarde: N/A or F
Xerneas has antlers, which, despite this Pokemon being very beautiful and graceful, I can only associate with stags (male deer). Yveltal is female, oddly, even though the Y chromosome only belongs to males. The vulture/bird of prey design, ruff of feathers around the neck, and red coloration solidify my opinion of it. Lastly, Zygarde looks completely primordial but it's also a serpent, therefore it's either female or genderless.