Well, the majority of my Pokemon are going to be male, but there are numerous ones that I'm reserving as females. For instance, female Chikorita in HGSS! I am not taking a male Chikorita, since that just looks too weird. Or freaky weird, as Lucas would say. Pokemon with proper genders that match their sprite(s) FTW! :)
On another note, it does seem kind of cool when a Pokemon's gender can't be defined merely by sprite. Lugia, Ho-Oh, and Mew are some examples, in my case (though Pokemon 2000 technically made Lugia a male).