The question, to me, means "What does upset you?", but I would like to know what kind of contraction "'s" is. Is it "does"! or "is"? and then, how do we explain the development of the original sentence to the current form? By the way, the sentence was taken from an example in the Cambridge Advanced Learner's Dictionary; it is "You're very crabby today. What's upset you?"
It isn't "does" or "is" but "has". "What has upset you?" is the full form. In my mind use of this contraction is only used in informal, spoken English (the sort where you might see words like "gotta"), and should be used only in casual settings.
As for how it became a contraction, I suppose they just shortened it, keeping the
s from "has". Most of the time you see
's in a contraction it stands for "is" but this is an exception (note that most exceptions to that rule will be in more informal, spoken English).