Female most, these days.
It's funny, when the gender thing was first introduced in Gold and Silver, I was a little bratty boy and was like "Ewww, I don't want GIRLS on my team!" I absolutely refused to raise female pokemon. Later on, when I got hooked on the Battle Tower (and just battling in general) I realized my team was weak to gender based moves, so I started forcing myself to raise both genders. And now, I like to breed pokemon; females determine species and also pass natures w/ everstones, so I capture female pokemon more. In fact, I seem to like having female pokemon on my team more than males these days, which is really strange to me, considering that I used to only raise male pokemon.
I still have gender preferences with some pokemon, though. I generally prefer a female Milotic because, hello, it looks female! Same preference with wanting a male Syther/Scizor, female Eveelutions (which are rare...:(), female Butterfrees, male Gengars, ect. But this is all just preference; it's not a hang-up like when I was little. If I have two of the same pokemon, one male, one female, I choose the strongest. Period. Well, unless of course I completely lack a certain gender on my team, but that goes without saying.
And um.........I didn't realize until fairly recently that there are female Machamps. o_O That's just creepy.