Possibly the easiest way to do this manually I guess would be to set up a simple rig that approximates the eye setup.
Put two cameras in your scene (CameraLeft and Camera Right). Parent them to a Null object (Null_CameraMove) and set their positions to the same X/Y values and the appropriate separation on the Z axis. These are now your 'eyes'.
Add another Null to the scene (Null_CameraTarget) and make this the target object for both the cameras. Now, simply use the two Null objects to move and focus your cameras.
Make one render out with the left camera, then set the active camera to the right camera and re-render - voila - two separated sequences ready for running through an anaglyph filter....
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