A note on setting up stereo cameras:

The reason the cameras for the left and right eyes need to be aligned parallel to each other (rather than angled in such that their axes intersect at the center of the display screen) is that:
• Each camera axis is perpendicular to its plane of projection
•  If the cameras are not parallel, their planes of projection do not coincide, so vertical parallax results
To see the relationship between vertical parallax and each eye's plane of projection, consider the example of a rectangle oriented parallel to the plane of the monitor so the z-axis passes through its center (the rectangle is the maroon line in the middle of the image below).  In this example, from the right eye's perspective, the projection of the right side of the rectangle will be taller than that of the left side (since the right side is closer to the user but the same height as the left side).  Similarly, from the left eye's perspective, the projection of the left side of the rectangle will be taller than that of the right side.  It seems reasonable that this vertical parallax will be uncomfortable for the user.

(figure adapted from Paul Bourke's Calculating Stereo Pairs)

References:
1. Stereographics's Stereo3D Handbook
2. Paul Bourke's Calculating Stereo Pairs

Eric Karasuda (& Sara McMains)