These are my opinions regarding their genders. In case it's too hard to determine a gender by their appearances alone, I'll try to visualize them as Gijinkas. Of course, I'm skipping those that do have genders.
Legendary Birds: I dont know why, they just seem like they're all male to me.
Mew: At first, my opinion was that mew should look like an Androgynous boy or or a Tomboyish girl, but Snowdrop has a very valid point: Mew is an Embryo. At this stage of life, all humans are female. In the mother uterus, the first stage of life is the Embryo being molded in a basic shape, and the information for this basic shape is guarded inside the mother's DNA, which means that this basic shape is that of a female being. Only in later stages of life does the Embryo checks it's own chromosomes, and if they're the equivalent to a male human's chromosomes, then it starts developing as a male. What does this mean is that at the start of their lifes, everyone is female, and only later some of us become male. But anyway, as an Embryo, I think Mew should be female.
Mewtwo: I always thought of Mewtwo as male, even before seeing the movie. What really defines Mewtwo's gender however, in my opinion, is whether you see him as simply an enhanced clone of Mew (in which case he would too be an Embryo, albeit a modified one, and therefore a female) or as an adult form of Mew, whereupon his gender would be, well, whatever you think, and as stated above, I believe he is male.
Legendary Beasts: Same as the birds, they all just seem to be male to me.
Lugia: Although I believe that there are more than one Lugia, and they could be male or female, as an indivindual, I see Lugia more as a male.
Ho-Oh: Same as Lugia.
Celebi: Hmmm... well it depends. I can imagine Celebi being either male or female, although to tell the truth, only it's shiny form seems female to me. So I'll say both
Legendary Golems: The golems are hard to say. I can't determine their gender by their appearances, and trying to make Gijinkas of them would't help, as it would be like humanizing a rock. They have no defining features that could be integrated in a Gijinka design. It's hard to try to make a humanization of something that has no human characteristics whatsoever, specifically a face, which other mineral pokémon such as glalie, geodude and heck, even magnemite have (in case of magnemite, it's single eye is enough). Note that the three pokémon I cited are of the same type as the Golems. I'll have to do what you guys have already done and classify them as genderless.
Weather Trio: As simple pokémon it's hard to determine. As seen in the anime, they apparently don't have the same human-like intelligence as other pokémon, and seen to be nothing more than irrational beasts doing nothing more than instinct tells them to, which, apparently, is increasing their domain and destroying things, and you don't ask yourself whether the vultures waiting for your death are male or female. If I try to make them as Gijinkas, I'll have to say that their bodies remind me of some kind of armor, and I would see them all as knights, so I guess to me they're male.
Jirachi: I can't see him as anything other than male, I dunno why. It's probably because when we think of a random person of unspecified gender, we imagine it as if it were a man, a wrong assumption carved into human mind for eternity.
Deoxys: The thing with Deoxys, is that... well. Did you watch the movie? Remember that that losangular light ended up being a Deoxys? The thing is that Deoxys in itself isn't a pokémon, but rather an alien race, and he only turned into a pokémon as we see him in the games after absorbing pokémon DNA, and considering that his true form appears to be made of glitter, I'd say he is an either asexual or hermaphrodite life form. So, I'll have to say genderless.
Lake Guardians: Azelf, Mesprit, Uxie. To me, it seems only natural. Also, that's how they are determined in Mistery Dungeon.
Creation Trio: Hmmm... That's hard to say. Or rather, I could easily say male, but that would be by the same reason I see Jirachi as male. Considering that they're like the pokémon world equivalent to Angels (being created by God to shape the universe), I guess I can say genderless.
Darkrai: Male. Same as Jirachi.
Manaphy: Female, because it looks like one to me. Although, there was a male Manaphy in Mistery Dungeon Time/Darkness/Sky.
Regigigas: Same as the golems, obviously.
Shaymin. Going by appearance, it's Land Forme looks female to me, while it's Sky Forme looks male.
Arceus: Genderless, simply because God is not supposed to have any gender. Although I can totally see that hair of his as a big cool beard, or a "Marge Simpson" 'do.
Victini: I've never seen him on any movie or game that might show me any glimpse of his personality, so I'll have to say male, and unlike jirachi, it's because I really can't see him as female.
Legendary Musketeers: Male, because they're based on male characters.
Zekrom: I'd say female because he is based on the Yin, but eff that, he looks too masculine to me. Male!
Reshiram: Male, it looks like one to me, plus Yang and all that.
Kyurem: Dude's an effing corpse, an empty one in fact (Zekrom and Reshiram came out of him). Sure some of you might disagree with that, but I agree with this theory, so I'll say genderless for the same reasons as Shedinja.
Meloetta: Female, well, duh.
Keldeo: Same as Musketeers, 'cus he's one.
Genesect: I disagree with people saying genderless just because he was modified. He's an android sure, which means he retains the gender he had from before alterations (remember, gender and sex are two different things. he could lose reproductory organs and still retain it's gender). I'll have to say male, because I can't see him as a female.
Well, those were my opinions, with the important parts highlighted for those who have the "tl;dr" mentality.
