Primarily it's a bit of an in-joke amongst friends, it's a phrase that we associate with this guy we used to know (a good few years ago) who would often use it when bumping into you somewhere out and about. It always sounded like he was surprised you were there or as if he was suggesting you oughtn't to be wherever you were, you know...like a pub, a gig, a shop or other such exclusive venues. He would also say it in his Donald Duck on helium voice (which wasn't an affectation, it's how he actually sounds) and it would often be accompanied with a squelchy tap on your shoulder. I shudder even now just thinking about it. Many of us came to dread the shoulder tap. He had an uncanny ability to turn up when you'd least expect it, like the baddest penny there ever was. Nowhere was truly safe. You could try and hide in a cupboard but he'd probably already be in there, waiting...tap, tap!
The same question is also used over and over again in many TV shows, listen out for it, if you've never noticed it you probably will now that it's been pointed out. It's just one of those things that people don't often say in reality (apart from the aforementioned accquaintance) but is ubiquitous on the telly - much like "Let me get this straight..."
Update: Looking back at it this may come across as being a bit mean about the person in question, but I'm not going to change it as it does sum up how things seemed at the time.