Some people get sick watching 3D movies because the signals sent from the eyes to the brain do not match the signals sent from the inner ear. The eyes are reporting motion, yet the inner ear does not sense any motion, and thus the body becomes confused and nauseous.
The inner ear contains a small section that is filled with a thick, viscous liquid that slowly moves about as the body moves. This area is also lined with thousands of small hair-like receptors that detect when the liquid moves. These receptors transfer the information about the moving liquid to the brain, and thus controls the body's equilibrium. This area is responsible for alerting the brain of physical motion and compensating the center of balance.
When a person sees motion in front of them, especially in the form of large 3D objects simulating the experience of full body motion, the eyes send signals to the brain that the body is in motion. The sick feeling occurs when the brain thinks that it's moving because of the eyes and begins to compensate for motion but receives conflicting messages from the inner ear. The body tries to be in a state of motion and rest simultaneously, which causes the person to become nauseous and feel off balance.