A categorical question that can only be met with an amorphous response. See the thread in November-December on this issue.
As was pointed out earlier, the "top ten" that suits your aspirations will vary from someone else's. With that in mind you have to first ask yourself the questions: "Do I want to be an academic surgeon, or go into practice?" A corollary would then be "Do I want to pursue fellowship training?" And again will that be in the context of an academic career or not?
I'll assume that you're asking about programs that will specifically prepare you for being on the faculty at a university-based medical center with the inherent responsibilities for research (i.e. getting grants to do that research), publishing that research, teaching, and seeing patients in a tertiary care setting (though many patients will be bread and butter cases). Naturally there will be heated debate about these.
Starting from the right upper corner of the country (geographic order):
Brigham & Women's
Massachussetts General
Cornell (or Weill, I guess)
Univ. of Pennsylvania
Univ. of Pittsburgh
Johns Hopkins
Duke University
Washington University
University of Michigan
University of California-SF
This list is absolutely arbitrary. I certainly won't pretend to rank those within these 10 though. I'll just mention that issues should be weighed when comparing a place like UCSF that has some of the best basic science in the world but is clinically a hair below a Duke that has always been stronger in the clinical arena.
People will be hollering and screaming about up-and-coming programs, or "regional powerhouses", or the fact that a couple of the programs I listed have new chairmen who haven't had a chance to impact their institutions either positively or negatively.
The programs I listed are those that explicitly see their mission as training future leaders in academic surgery, and have a proven track record in carrying out this mission.
Note that all of them are associated with university medical centers that have extremely strong research enterprises (Duke, Pittsburgh, and UCSF are the top three in NIH funding within their Departments of Surgery). There are scores of Programs that train oustanding surgeons that are "thinner" in the research opportunities available to residents on campus. A good number of the programs I listed pretty much expect two years of research.
If clinical acumen and competence is your sole criterion, the list expands to scores of programs.
(Edit: Syntax)