Croseye tutorial for 2D software.

"3D images are easy to do with 3D software, you just render with two cameras set up separated like eyes, and then stick them together with the right eye image on the left and left eye on the right.

You can also make a simplistic version if you're using a 2D software that supports layers (I use The GIMP, but I assume many others can be used the same) you can have things at different distances in different layers and move them left or right for each eye. You need to move things that are closer than the focus left on the right eye image and right on the left eye image proportionally to how much closer it is to the viewer than the focused object. You of course, do the opposite with objects further from the viewer. "

http://www.flickr.com/photos/kiml42/6078055998/