They can both mean "congratulations" or "well done", but "good on you" is rarely heard outside Australia. Typical use: "You got the job? Good for you!" (An Australian would say, "Good on you, mate!")

"Good on you" usually is used to refer to an object or anything that suits a person well... e.g. The dress looks good on you. "Good for you" is pertaining to a particular situation that the person deserves. e.g. person 1: I passed the exam! person 2: Good for you.