Happens all the time; even HMS's MD/PhD has to go to its waitlist. You might want to contact each school to see where you are on their waitlist (if they will tell you), and what kind of a chance you have. Ask them about movement on their waitlist over the past few years. If you are holding an acceptance at another school, you can tell them that; it might get their competitive juices flowing and make you more attractive in their eyes (the Bathsheeba effect).
You probably want to communicate with the school you are most interested in and let them know that you will definitely attend if accepted. Schools that utilize waitlists like to make their admissions stats look good, and would rather offer a position to someone who will definitely accept rather than "waste" it on someone who might turn them down, all other things be roughly equal. (Hey, admissions officers are people too, and they do not thrive on rejection.) It probably would be major uncool to pledge your troth to all the programs you are waitlisted with. Notwithstanding the virtues of honesty, a couple of the programs might communicate with one another and you could end up hacking off both programs and losing your chance at admission.