It can be used in a positive or negative manner. I'll give you an example of each.
Positive, as another way of saying, "Good Job":
"You finished your project a day early and it looks fantastic. Wow, way to go!" In this case, the speaker is happy with the product that the other person produced.
Negatively, in a sarcatic manner:
"You dropped the ball on that one. Way to go, Einstein." In this example, the person speaking is using heavy sarcasm. Dropping the ball means messing up, so we know when the speaker says, "Way to go," it has a negative connotation. Albert Einstein was brilliant, but here it is used sarcastically.