I have written a small python script to generate stereograms from blender.
If you are interested, download
http://www.sulyok.hu/~peti/blender/stereogram.py and put it in your scripts dir.
Then download http://www.sulyok.hu/~peti/blender/stereogram.blend.
Choose Scripts -> Update Menus.
Choose Scripts -> Wizards -> Stereogram
Press Generate in the scripts window, and see the result saved as stereogram.tga.
I would like to know what you think about it, or if you have some suggestion.