The process described here works with Hugin 2010.4.0 with the patches from bug 679753 and 702135.
Let's start with two images taken from slightly different angle, named left.jpg and right.jpg:
align_image_stack -p aligned.pto -a aligned -m -i -P -C right.jpg left.jpg
The newly added stereo options are:
-i optimize image center shift - this compensates the perspective distortion when the lens are not parallel.
-P align the "stereo window" and try to create the "pop-out" effect
-C crop the images to the area covered by both images
The result can be converted for example to anaglyph:
composite -stereo 0 aligned0000.tif aligned0001.tif aligned.jpg
When we don't like the result, we can open the pto file in hugin and modify it. For example we can improve the pop-out effect.
On the photos you can see that the closest point is near the lower edge. The automatic process identified it as point 161 and marked it as the only "normal" point. After optimization, this points has zero shift between images and appears at screen level. The rest of the image appears behind it.
We can delete this point and choose another, in this case 137:
Then, after re-optimization, everything in front of point 137 will appear like popping out of the screen. There is still a problem with the lower edge where the stereo window is broken. We can fix it by crop:
Note: there is some problem with reading the optimization parameters into hugin, so for now it is necessary to add New Lens for the second image before running optimizer:
Finally, here is the result: