I started experimenting with aerial stereo photography on long flights. I have always preferred a window seat and enjoyed the view more than the in-flight entertainment.
The process is very simple: take a two successive images as the plane moves. I have found a second or two between exposures is sufficient to create the parallax needed for a 3-D image: the closer features are to the aircraft, shorter the time between exposures is required. I attempt to maintain the composition of the main elements between exposures. The challenge in holding that composition comes from turbulence or aircraft motion.
To make the stereo pair, I simply combine the images in Photoshop. Which image is left or right depends on how you view the stereo pair and the direction of travel of the aircraft. I prefer fusing the images by crossing my eyes, but others prefer looking through the images. If you have the images in the wrong order, it will be apparent when viewed.
Click on the link to view more stereo pairs: Aerial Stereo Photographs