Being that I always use Ditto for breeding, I don't care when it's breeding related. It typically depends on the stats, and the type of pokemon it is. For example, if I have an espeon, I'd prefer it to be female, since espeon comes as more of a female pokemon to me.
Also, since they sometimes have slight stat differences with genders, I might like one's stats more than the others :P
Although, that may just be a coincidence, as I have caught about 40 bidoof, half and half (took a while -_-), and looked at their stats to see this theory, and by the results, I still guess that gender may have a part in it.