"How come?" isn't exactly the same as "Why?", although the two are often interchangeable.

"How come?" means "What are the general set of circumstances that have led to this situation?" and there is usually an element of surprise. Here's an example :

Let's say that your friend told you that she was going on holiday and wouldn't be around in your town at the weekend. You go to the cinema at the weekend, and you see your friend there. You're surprised to see her.

In this situation, you wouldn't ask the straightforward "Hello. Why are you here?",  because the answer would be obvious - it goes without saying that she's there to see a film. But you might say "Hello. How come you're here?" . (No inversion, as Phil pointed out) Unlike a simple "Why?", the question "How come?" enquires about the broader situation - the circumstances that led to her being at the cinema that evening instead of going away on holiday as planned.

I hope that answers your question.

It just means "why." We use it all the time. Grammar: no inversion. Compare:

Why are you here?

How come you are here?

With SuKi around, I might as well take a nap :)