Hugin is the only free alternative to AutoPano Giga/Pro that I have found. In these cases the number of photos is smaller (and mostly horizontal). This tool is not as good as AutoPano in guessing the position of photos, but does a good overall job.
These are my two first experiences with AutoPano Giga. They have plenty of problems. One of the photos has a lot of inconsistencies, most of which are my fault, for moving while taking the photos (and not just rotating over an axis). Nevertheless, I like these pictures.