It's a rude way of confronting someone that is looking at you. For example, if you are on the train in a really bad mood and someone across from you keeps staring at you, you might look him in the eye and say "what the hell are you looking at?". Keep in mind this is quite rude and you are probably better off not using it.
Of course, literally it just means "what are you looking at", but with extra emphasis. Technically the other person doesn't have to be looking at you to use it, but as a phrase that's usually what it means.