Deep Sky Stacker is a free application for the calibration, registration and integration of deep sky images. It was my favoured stacking application when I first started this hobby, but I moved on to AstroPixelProcessor because of some of the limitations of DSS.

One thing that DSS is not able to do is deal with images taken at different scales. It only works with image sets taken using the same camera and optical system, which for many people isn't really a weakness at all since they may only have a single set of equipment.

You can learn more about DSS on its website, which also includes some good information about the process of calibrating and integrating images.