Actually I have no special reason not to apply to Stanford. I just think that the research interests of the professors of these other places are more compatible with what I want to work with in my PhD. Vijay Pande, for example, develops theoretical methods to study biological systems, and Hans Andersen is more in to statistical mechanics of liquids, which are fantastic subjects, though not the first ones on my list.
Prof. Martin Head-Gordon would probably be my first choice to work with at Berkeley. Although, I might also be interested in working with Professors William Lester and William Miller.