Unix software
Basic Library
Panorama tools is a high quality and free panorama stitching software package. Notably it contains pano12 and PTOptimizer, both required by Hugin.
Stitching Software
Hugin provides an easy to use graphical user interface for Panorama tools. Available for most Linux and Unix varieties (plus OS X and Windows)
Helper
autopano-sift: Automatically identifies control points. Works with Hugin
PTStitcher: The original Panorama Tools rendering engine, now superceded by nona
nona: An open source replacement for PTStitcher. Part of the Hugin package
Enblend: Overlays images so to make the seam invisible. Works with Hugin
ImageMagick: Optionally batch process images before using Enblend, e.g. when you have large black areas because of a pitch angle.
PanoCube: Converts equirectangular (360x180) panos to QuickTime cubic movies.
Viewer
Quicktime can be installed via wine
Plugins for the Gimp
The Gimp is a sophisticated image editor similar to Photoshop.
There are several panoramic photography related gimp plugins that can be used to manipulate panoramas.
Non-Panoramic use
clens command-line version of PTLens
Other Software
PanoPoints: Perl-Based control point picker for use with Panorama Tools