These are not my own, but I had saved them a few years ago from posts on SDN:
GI:
Hopkins
MGH
UCLA
Michigan
Pitt
Wash U./Stanford/Northwestern/Oregon
Florida/Virginia/Southwestern
Boston has a little bit more to offer as a city than Baltimore, though Baltimore's image has changed over the years. It depends on how interested in basic science you are as MGH is a very research oriented place and the GI fellowships are often extended an extra year to accommodate the research. UCLA is truly a top-notch program and has the benefit of being in LA, but with that comes significant cost of living that is difficult to afford with fellow salaries. Michigan and Pitt are both phenomenal programs in their own right and both have a good balance of the different GIspecialties. The others are all great programs, but I feel less able to distinguish between them.
For academic prestige (CV booster):
Hopkins
MGH
UCLA
Michigan
I'm single and want to date (i.e. desirable cities, lots to do):
MGH
UCLA
Northwestern
Southwestern (tons of people in TX)
For low-cost of living:
Pittsburgh
U. Florida
Southwestern
Virginia
I love the outdoors:
Oregon
Michigan
GI:
Not a top 10 list by any means, but rather a partial list of programs that my colleagues and I liked last year and would strongly recommend a visit... They all have their strengths, relative weaknesses, and idiosyncracies, but really all are very good programs. YMMV obviously, depending on your career goals. I would say that my colleagues and I mostly looked at academic programs, though some of us wanted research tracks while others looked at clinician educator pathways.
Grouped by region and in no particular order (other than what popped into my head first):
North: Penn, Johns Hopkins, Mt. Sinai, all 3 Harvard programs, Yale, Pittsburgh
Midwest: Wash U, Michigan, Mayo Rochester, U Chicago, Cleveland Clinic
South: Duke, UNC, UT Southwestern
West: U Washington, UCSF, UCLA
There are many other programs with good-to-excellent reputations such as Florida, MUSC, Indiana, Stanford, Columbia, etc. but unfortunately I have neither first- nor second-hand knowledge of them.