The advice I was primarily given was to choose the best programs in your general region, except that the Big 3 programs can be equal to or better than the best programs in your desired region.
From my experience and personal opinions on the interview trail, this is what I thought were the top programs by region:
Big 3: MDACC, MSKCC, HROP
East: Penn, Johns Hopkins
Midwest: Mayo, WashU, Michigan
West: UCSF, Stanford, UCSD
South: Duke, UNC, Florida
Next tier below:
East: Yale, Maryland
Midwest: Cleveland Clinic, Chicago, Wisconsin
West: UCLA, Colorado, OHSU
South: UTSW, Emory
Some other rankings of desired locations:
NYC: MSKCC >>> NYU = Sinai > Montefiore > Columbia >>> NYP = Downstate = Stony Brook
California: UCSF >= Stanford > UCSD >> UCLA >> USC > Kaiser = Cedars Sinai > UC Davis, City of Hope, UCI, Loma Linda
I may ruffle some feathers but this is just my 2c.