http://en.wikipedia.org/wiki/Auditory_system has the basic statement. Your outer ear lobe (the pinna) is shaped and convoluted in such a way that sound is differentially attenuated depending on its point of origin.Your brain's auditory system can make use of the different frequency spectra of the signals from each ear, as well as the overall amplitude and phase differences, to perform three dimensional localization.Unfortunately, when you use headphones, the sound source is directly against your ear lobes and directed straight into your ear canal. There's no opportunity for the pinnae do to their normal job of attenuation and distortion necessary for three-dimensional auditory response. There does exist signal-processing software which can apply the "human average" attenuation response to the signals going to each headphone. This can provide a simulated "surround sound" experience to the listener. I found a decent article from Dolby Labs via Google.On a side note, unlike most mammals, humans do not have the ability to move or rotate their pinnae. That ability provides far more precise localization for other mammals.
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Well I see that Cameron has beat me to it, but that was going to be very close to my comment. Think about how you hear a car approaching. In real life, you can tell that it is truly behind you. With only stereo sound, it is coming straight into your ear, but if you are in a room with surround sound, it would be simulated starting in the back speakers and moving its way forward. That isn't really possible with only two fixed speakers.
It could, but only if they had a gyroscope or accelerometer to determine which way your head is pointing. If your head was clamped in one position, you would get close to stereo sound. However, when you move your head, your brain can tell that the sound gets slightly louder in different directions. In addition, the shape of your earlobe affects the sound depending on the direction from which it comes. Your brain takes these slightly different sounds into account, and essentially builds up a 3D sound image of your environment.