Since I worked for a year on the graduate admissions committee for my department (EE) at Stanford, I can give you some idea of how it's done. That year, we had 5,000 applicants. The first cut was done solely on GRE scores and normalized GPA (we adjusted for known "grade inflation"). That got us down to 500. We then threw out all of the numbers and asked "okay, what else did you do?". People who had been active in campus groups, fraternities, did projects, worked on the side all got a big boost, as we cut to the final 200. That was for the Masters program, and of those, about 70 would make it into the Doctoral track. And of those, about 40 would actually finish.
I have been going through the law school admissions process this year. Top schools like Stanford, Yale, Columbia, and Harvard could fill up their entire classes (several times over) with people with 99th percentile LSAT scores.