Do applicants who are exempted from paying application fees get any other benefits Several universities waive graduate application fees for certain applicants who participated in a specific program or belong to a certain organization. My question is: do these applicants get any other benefits or considerations in the application process, or is the application fee exemption the end of the story?

Example of one of the universities that offers this:
http://grad.berkeley.edu/admissions/apply/fee-waiver/
I've served on a doctoral admissions committee and we were not made aware of these fee waivers or special organization ties unless the individual directly wrote about them in their statements of purpose or resumes.