This is my take on the top 9 residency programs based on reputation from what I gathered from attendings, residents, and medical students. I believe that the top 10 programs based on reputation will be different from the top 10 popular programs. I think geography plays an important role (if not more important) than the reputation of a program. I already spent four miserable years in bone chilling coldness for graduate school (I went to Mayo and took a few years off) and want sunshine, water, and mountains for a change!
In no particular order:
(top 9 because I can't think of anymore at this time)
BWH/MGH-Boston, MA
UTSW/Parkland-Dallas, TX
UNC-Chapel Hill, NC
UCSF-San Francisco, CA
Northwestern-Chicago, IL
UW-Seattle, WA
Brown-Providence, RI
UAB-Birmingham, AL
Pitt-Pittsburgh, PA
I did not include Mayo on the list above for residency programs but I would say it is a top 3 fellowship program for gynecologic oncology. Mayo Clinic is more of a place you would go for fellowship or a faculty position (I heard this is true across specialties).