The DSi has cameras, which means the 3DS will have to have them too if it's going to be backwards compatible. We've also heard rumors that the "next DS" will have tilt-sensors better than the iPhone. With either the camera or tilt-sensors either of these 'faux 3D' systems would work. But since we've seen the DSi do this already, it doesn't seem likely that the new hardware will rely on the same old trick.
Enter our friends at Engadget, who uncovered some details from Japanese newspapers. If they're right, the Nintendo 3DS will incorporate parallax barrier LCD screens from Sharp (see also this explanation of dynamic parallax barrier screens). This is the same technology used in a few "3D Laptops."