Flash photography lends itself perfectly for 3D photography: the flash ensures that the two photos that make up the anaglyph (stereo image) are taken at exactly the same moment in time. Simply place 2 cameras with the same focal length (preferably identical cameras with identical settings) and point them at the same scene.
By using a simple Matlab script, the red and green+blue channels are mixed to make a 3D image that must be viewed with red-cyan (or red-blue) glasses.
When you first make black and white images of the two photos, you can make a black and white anaglyp. For some situations this is the only solution: take for example the bright red tomato. You simply cannot expect that to work with red-blue glasses (nothing will pass the blue filter).