The phrase probably originated as nothing more than a self-referential version of an expression normally directed at someone else, which puts it in the same category as "Shame on me!" (after doing something wrong), "Bless me!" (after sneezing), or "Happy birthday to me!" (at a birthday party). There is an element of childlikeness (or childishness) in the formulation because children sometimes take an expression that is normally outwardly directed, and instead direct it toward themselves. So it's entirely possible that the speaker imagines that saying "Good for me!" is a disarmingly cute way to respond to receiving a favor.
Nevertheless, I think that "Good for me!" does have an element of crowing to it—especially if it occurs in place of, rather than as an adjunct to, an appropriate acknowledgment of your effort, such as "Thank you, Tom." But at least it produces a somewhat lower reading on the gloat-meter than, say, "Yay! Free labor!" or "Hooray for chumps!" Ultimately, the tenor of the expression depends largely on your relationship with the person who uses it.