Most programs accept or waitlist through the department (phone, email). Rejections often come through the Graduate School and take much longer. If there are a bunch of acceptances and waitlist notifications out for your school(s) already, your chances aren't good. At least, that is my experience. Some schools may keep a group in reserve, but often it's simply that the rejections haven't been sent by the grad school yet. If you are uncertain and trying to make a decision, you might call the dept and see what the situation is (less annoying than emailing the DGS, IMO),