I think most schools have a general goal of the number of students they want to admit to their program for a coming year. Say for example, say Department A is looking to bring in about 20 students a year. If in the past years, they have found that about 50% of the people that they accept will decide to come to school and study in Department A. So Department A sends out about 35-40 acceptance letters in the first wave. Department A also sets aside a separate list of candidates, the wait list, which they dig into if they don't achieve their quota, or decide that they want to raise their quota a bit. So in the example given, if only 18 of the admitted students decide to come to Department A, then Department A will dig into their wait list to try and get to 20ish students.
To answer your question of what your chances are would be hard. It would depend on how many students Stanford's CEM program is looking to take for Fall 2011, and your position on the waitlist (some schools rank applicants on the waitlist)
Disclaimer: I'm not 100% sure what I said is right, but it is sort of the assumption I made after reading through these forums the past few months.