I wonder how many of you that posted actually interviewed at these programs.
If you asked me before interviewing, my ranking would have been seriously out of whack (Stanford's MSTP would have been a top five).
The problem with a top 5 or even a top ten is that it really depends on your criteria and what field of research you're familiar with.
Find a general field of science you like: Engineering, Translational, Basic Sciences. Narrow down that field if you want to even more i.e. materials engineering, biochemistry, immunology, cancer.
Secondly, you want a very strong and respected medical school. There is no sense in joining a MSTP that has poor clinical training, unless you plan to go straight post-doc. If you want to get even more discriminating, then narrow it down into a general specialty (pathology, internal medicine, even surgery).
Finally, you want a program that is well funded (private funding is almost a necessity these days), well run, well experienced, and has a history of accomplished graduates (a side note: you need to know whether the MSTP at a particular school is well respected intramurally).
Those are the main points that go into figuring out the best program for you and you alone. It differs between people.
Now if you want to argue what the best program is for, say, cancer biology, then go for it. But as an overall ranking? That's just absurd.