I did something like this a while back~ It's mostly based on appearance, voice, or information from the side games.
Male: Zapdos, Ho-oh, Kyogre, Groudon, Rayquaza, Deoxys, Uxie*, Azelf*, Dialga, Palkia, Giratina, Darkrai, Regigigas, Reshiram*, Zekrom, Arceus, Cobalion, Kyurem, Latios, Thunderus, Tornadus, Landorus, Hoopla, Volcanion, Keldeo, Xerneas, Yveltal, Zygarde
*Uxie and Azelf were originally considered female, but are now considered male due to being referred to as such in Pokemon Mystery Dungeon Time, Darkness, and Sky.
*Reshiram is said to have been designed to look feminine, yet sounds masculine in the movies, and is considered as such.
Female: Articuno, Moltres, Raikou, Latias, Mesprit, Cresselia, Victini, Virizion*, Diancie
*Though Virizion is said to have been based off of a male, almost everything else about it suggest female to me, including appearance and voice. Also referred to as Female in Pokemon Mystery Dungeon: Gates to Infinity.
Mostly Male: Entei, Suicune, Registeel, Regirock
Mostly Female: Mew, Celebi, Regice, Shaymin, Jirachi*, Manaphy*, Phione, Rotom
*Jirachi in the Anime was called a male, but otherwise appears feminine (as was the case in one of the dubs of Jirachi Wish Maker).
*Though Manaphy is called the Prince of the Sea and the one in Pokemon Mystery Dungeon was referred to as male, it seems to be a very feminine looking and sounding Pokemon.
Mostly Male and Mostly Female refer to legendaries of which multiple have been seen and equate to the 87% male/12% female ratio and the 75% female/25% male ratio. Based on appearance, behavior, and voice.
Both: Mewtwo*, Lugia*, Heatran
*Mewtwo: The one in the first movie was clearly male, while the one in the Genesect movie seemed particularly feminine. Though, since I call the latter's canonicity into question, I generally consider Mewtwo as male.
*Since Lugia (Silver's mother) and Silver in the Anime exist, female and male Lugia must exist.
