Autopano pro is an integrated panorama stitching software for Windows by Alexandre Jenny which automatically finds and stitches images.
It is based on a research project called Autostich that was developed by Matthew Brown and DG Lowe; the research paper was originally published in 2003. Autopano Pro is one of the few commercial licensees of the Autostich engine. A free tool using the same technique is autopano
The software can, for example, given a folder with images composing 2 different panoramas, detect that there are two different scenes represented by the images in the folders, and actually stitch all of the images together to create 2 panoramas. This has great implications for batch processing, as the entire stitching process can be completely automated in many cases.
The image below was stitched automatically from 42 images shot handheld from a cellphone, which gives you an idea of Autopano's detection, alignment, and stitching capabilities.
The software also has other advanced features such as distortion correction, Color Correction, multiple blending modes, HDR support (although it is limited at the moment), verticals alignment, cropping, re-centering, and much more.