The screen has twice the horizontal pixel density of any other screen, which allows one set of lines aimed at one eye, while the other set is aimed at the other. The 3DS renders a single frame twice, each a different viewpoint, interlaced between each other vertically. Because of this, each eye will see a different frame, and your brain puts both of the frames together as a 3D image.
This results in the game actually running at half the frame rate that it's running internally; to make a 60 fps game on the 3DS, the developer would need to be able to make it run at 120 fps in 2D. However, this does not take up half the power of the console, which is just an urban myth. However, this shows the advanced power of the hardware, which is capable of rendering high end shaders, lighting, shadows, textures, fur, bump mapping, normal mapping, and other effects in real time with ease.