Mipple,
I'm also on the Stanford waitlist, and I'm wondering about a lot of the same things you are. I've heard differing rumours about the waitlist. Some say that the alternate list is made separately for those people that Stanford wants to accept but doesnt have room for late in the interviewing season. But I have also heard that the adcom actually makes the alternate list from people that are pulled from the waitlist. I really want to believe this, but it also makes sense: why would they make a waitlist they have no use for? In any case, someone in the admissions office told me that they won't even begin to look at any of this business until July (!!!).
I don't know any specific numbers about rejections vs. waitlist decisions, but from what I have heard and from what I've seen on SDN, it seems like Stanford tends to reject man after the interview, accept some, and waitlist few. Also, last year was a bad year for people on the waitlist - zero were taken off it (of course, not counting alternate list accepts).
I really liked Stanford, and I hope I get taken off the waitlist. But I have to say, their process is really really wierd and unnecessarily mysterious for applicants.