As mentioned before, it depends on the school.
Anderson: the only school that I have heard of that will average your scores if you take it more than twice; they take a tough stance.
Kellogg, Wharton, Harvard, Stanford, Darden, Haas, Chicago, Ross, Yale: to the best of my knowledge, these schools will either ask how many times you have taken the test, your two highest scores, all of your scores, or some combination of these criteria. All of them, however, claim that they look at your highest score. Chicago specifically frowns on taking the test more than 3 times, but they will still take your highest score.
Columbia, NYU, Duke: they just want the highest score, plain and simple
Tuck: allows you to put the highest breakdowns of your score, but I think, in the end, they use your highest score for class avg. purposes.
(Not sure about MIT, those who have applied can better comment on MIT, as well as other schools)
Just because a school asks whether you have taken the test more than twice does not mean you will get dinged if you have; most likely, they will get to see all of the scores in the end, whether they ask for them in the app or not. If you are a well-rounded app, then apply to the school that fits you the best.