I sent them to my top four--PD's and some interviewers, but I only did this because I am a lemming.
There are a lot of differences between programs as to how they approach the match. They do not all wait for applicant letters and chair phone calls before they make their lists. It's probably fair to say that some of them do wait, but there are lots of programs (some that I interviewed at) that make their lists immediately after interviews, especially the larger academic ones--some even said this at the interview. At the Univ of Mich they went so far as to discourage sending thank you notes, emails and phone calls because they said it won't change anything and they would not respond in kind. Remember, when you receive a 'glowing' letter from a program proclaiming your greatness, does it/should it change your rank list? No. True, I sent out letters or emails to my top programs and I have received letters, emails and phone calls but not one of them has changed my list--during one of the phone calls the PD even said that he didn't want me to tell him where I was ranking them, just that I was, in fact, ranking them. If I were a PD the only thing that would influence me is when an applicant actually states that my program is number one--and think about this for a minute; if you are not a highly competitive applicant for a program, or there are lots of other applicants they would rather have, then a call from God won't make a difference. You will not jump from the middle of a programs rank list to the top because you told them you were in their top three. I sure wouldn't believe anything but 'number one' if I were a PD.