Here is a list of programs the Program Director at my medical school put together by region when we kept asking him as 4th years what the best places to apply to were. He used the following criteria: academic reputation, research funding/lab opportunities, fellowship placement (where, how often, what specialty, (PedsSurg at Boston Children's/CHOP, SurgOnc at MSKCC/MD Anderson, etc), clinical experience (Livers, Whipples, Esophageal, etc.), academic/national reputation of faculty members, and general concensus among other surgeons. Our PD felt that training at these places would put us in good postion to match in to competitive academic fellowships. The list is not exhaustive, it is 2 years old, and it is just one PD's opinion. I'm sure it left some great programs off, but take it for what it is. Good luck with the match.
WEST: UWashington, UCSF, UCLA, Stanford, Utah, Colorado
MIDWEST: Minnesota, Mayo, Michigan, WashU, Wisconsin, Cincinnati, Louisville, U of Chicago, Northwestern
SOUTH/SOUTHEAST: UAB, Baylor(Houston), UTSW, Emory, UVA, Vanderbilt, Duke, Emory
EAST: NYU, Cornell, Columbia, BID, MGH, B&W, UPenn, Hopkins, Yale