H.G. Wells' alien invasion story is the most accurate scenario that I've come across. Unlike Hollywood's recent portrayals of aerial, naval, and ground battles (I'm still going to fork over cash for Battleship), any species that can traverse the universe would have technology far superior to our own. It'd be like attacking a stealth bomber from the ground with sticks and stones.
While I believe an intelligent being would recon a planet for biological threats like the common cold, a desperate species, which the Martians were in War of the Worlds, might not be as inclined. Ultimately, humans would suffer from biochemicals and diseases, not the aliens. Like their technology, their understanding of organisms, even if unfamiliar, would outweigh our own. They would cure and repair themselves faster than us, physically and mechanically, and if germ warfare is their tactic, they would probably design a super flu with our names written all over it.
In all likelihood, we wouldn't even see the aliens. They would not personally land. They'd park a great distance from our planet, out of range of any missile or shuttle we conjure, and send in drones or automatons. There would be no need to risk their own lives to take ours. Since we have drones and are currently working on robots/automatons, it's safe to assume a species in an intergalactic vessel would have them as well, for technological evolution is a hundred times faster than biological (rough estimate).
This is why I agree with Stephen Hawking about not even attempting to find another intelligent species or make contact. With what little we know about the universe, we have no clue whether or not the resources on Earth are rare. At this stage, it's debatable that liquid water is even needed for living organisms. If our planet's contents are unique, we're discovered, and a species is willing to cross the universe for them, we're doomed.
Let's not kid ourselves either. There's a whole lot of real estate in the cosmos. On earth alone, we have trillions of species ranging from single cell organisms to humans, and our planet, in the overall scheme, is young. It's only taken humanity half a million years to get where we are today. Think about the complexity of a species that evolves equally or faster than us, one that has been around for a hundred million years.
We can also forget a peaceful alien making contact with us any time soon. Aside from mass panic and the implosion of religion, we can't even coincide with each other. Imagine what would happen if a species that doesn't resemble us landed on Earth--it'd be shot or killed within an hour.
Would we have anything to offer an alien that they don't already know? I doubt it. If aware of our existence, spying on satellites, radio and television broadcasts leaked into space would provide them everything. Peaceful or curious aliens might study us like a field biologist, but I doubt it would go further. At best, we might stumble across an unmanned (lack of better word) probe.
Take all those theories into consideration and there's only one conclusion: we are probably not alone, yet it's best we stay alone. Unless, of course, you're into annihilation or servitude.