Obviously, I'm not alone in my plight, so I did some research on Stereo Photography. Here are my results from the Stereoscopy Wiki entry, which gives instructions on how to properly view these pictures;
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To view the crossed-eye view shown here, the viewer should move slightly back from his or her normal viewing distance and place his viewpoint on a line perpendicular to the center of the image. A finger should be placed halfway between the eyes and the image, then the finger should be viewed. The three bright spots between the pictures should become four spots, and the two images become three. If the focus of the eyes is now allowed to drift to the surface of the screen without uncrossing the eyes, a three dimensional depth illusion will appear in the central image. The finger may now be removed from the view. A viewer may find that the extra side images become unimportant once in-depth view of the central image is stable. This is a popular way of presenting images on computers but it is difficult to learn and for many viewers the method produces substantial eye-strain, and is not comfortable enough for extended viewing. Another disadvantage is that after prolonged viewing, the eyes may become accustomed to "close-convergence", as it requires the ability to direct the eyes as if viewing an object about eight inches away. This very close angle may lead to momentary double-vision. It also offers few of the advantages enumerated above that are provided by the stereoscope or Pokescope. When images are presented as for the stereoscope, with the image to be viewed by the left eye on the left, they can be viewed by diverging the eyes. This gives a different kind of "naked eye stress" than crossing the eyes (known as "wall-eyed divergence") but may require a smaller adjustment of focus, but can be even harder to learn. Without the use of viewing equipment, the size of a stereoscopic image viewable is significantly limited by one's eye-spacing and the inability of one's eyes to diverge painlessly. The major advantage of cross-eye viewing is that the images can be more than twice the area, and no glasses are needed by those who have the viewing knack. Prismatic cross glasses, with built-in masking, make the convergence very easy for most people, but they tend to be expensive, something like 5 times the cost of the simpler arcylic masking glasses.
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Yeeah, that's about it.