Interestingly enough, I pulled an investigation into the ratio of my Pokemon's genders yesterday. This included some legendaries (the ones I will most likely use) and Pokémon I don't have yet (all of the gen 5 ones, I already know which genders I want), but none of my shinies - only my main battling ones. The results were interesting.
As I expected, I have/will have more girls than boys - but the margin wasn't as big as I thought. Out of 132 individuals, 63 were female and 53 were male - only 10 more females. The remaining 16 are genderless.
I tend to go with the gender they look like most to me - male Reuniclus, Electivire, Heracross, Mantine, Swalot and Whiscash, and female Meganium, Togekiss, Cofagrigus, Lopunny, Wigglytuff and Ninetales. If they are hatched, given to me or otherwise rare, I'll take what I've got. Usually, though, I'll wait for the gender I want - gender differences or just overall appearance. Some masculine ones, though, like Salamence, Aggron and Lucario, are actually females - in fact, after training her, I now see Lucario as rather feminine. =]