One of the main problems with most current methods of generating and displaying stereo panoramas is that a stitched vertically wide 360 panorama pair in the usual formats (eg. equirectangular or cubic or cylindrical) cannot work in 3d properly when dewarped in an interactive viewer with views that are very wide angle and/or much tilted up or down. In fact with spherical 3d panoramas the view goes from stereo to pseudostereo as you rotate around the view when looking at nadir or zenith (so many people set the zero parallax point to be where the ground is with spherical stereo panoramas (and the zenith is often featureless in outdoor shots).
One way around this is to display such panoramas in unwarped form — i.e. with simple scrolling viewers. For example this Gopro 3d panorama I shot recently of a boat race preparation scene http://www.stereopanoramas.com/sydney2hobart.htm
Another way to view scrolling 3d panoramas is with Stereophoto Maker (free – Windows only) http://stereo.jpn.org/eng/stphmkr/ Just load the panorama as a stereo image (File/OpenStereoImage). Then go View/PanoramaMode. You can have the panorama scroll automatically with View/HorizontalAutoscroll. This can be used with a variety of stereo format panoramas.
Here is a Gopro panorama image you can try this out with if you like http://www.stereopanoramas.com/flugelmanana.jpg
This is done btw with a 4 second rotation. One thing to keep in mind with anaglyph jpgs is that normal compression methods lose 3d quality (as the color information is lost with most compression methods) but you can use the lossless color output of Stereophotomaker or convert from tif etc to jpg with Irfanview with its “Disable chroma color subsampling” option checked.