Sites like chesscube monitors you for some time if you comes under the radar of suspicion. They monitor how much time you are taking for hard moves and relative simple moves. If there isn't some serious difference, they may conclude you are cheating. Also I believe they implement some method to check the shifting between windows, however I'm not sure about what they use for it. But I personally know guys who had been banned. So their method is pretty good.
I second what JesperE say, You have to monitor the guy for sometime before arriving on an opinion.
