I recently listened to a dhamma talk by Andrea Fella about circumstances such as this that draws a strong correlation between the intention behind the act and the karmic consequences of it. The example she used was killing a spider. In one instance, you're just walking across the yard and you step on and kill a spider without even knowing it. There was no intention to kill. On the other hand, you see a spider in your house and with malice aforethought, kill it. Bad intention definitely present.
So...when you swat the skeeter, was there any thinking behind the act or was it pure reflex? Andrea went on to describe another example where a black widow (or a funnel web for you Aussies
) is about to descend on a sleeping baby and there is only time to swat it before it reaches the baby. Again, the intention behind the act is wholesome and not based on hatred, so...not bad.
(Disclaimer: During a talk, it was explicitly stated that the precept against killing says to "avoid" killing beings that "breathe". The big question in my mind is whether or not people in the time of the Buddha believed that insects breathe. I don't think I would have concluded that insects breathed back then and may not have even thought that fish breathe, but this is likely going to be the topic for another thread when I get around to it.)