Attached Link: Stereoscopic Thread.

Your in luck. I just happened to search for an old thread that we did about stereoscopic images. Jan. 2003. The thread also show how to create an anaglyph image using PS and the very last post has a link to an app that does it for you in all the different anaglyph types.The best part is it's Free.

Now I don't have PS so I don't know it it does batching but if it does there is one solution and I can't remember if the anaglyph app does batching. You still need to render each side and combine the two. I have not tried if you can parent 2 cameras together to create a constant set up. I would think you would still have to render each camera single.

See if that thread helps you some.