Serious nerdy talk ahead. You are warned.
When I shoot a panoramic image, I use a piece of software called hugin to take the pieces and stitch them together. hugin is free, and is designed to be a front-end for a bunch of other software.
Some of that other software includes the venerable panotools, nona, enblend, and autopano-SIFT.
Autopano-SIFT is a piece of software written to automate the generation of control points in stitched images. That is, it looks at a bunch of pictures and guesses how they overlap. It then tells other software what it learned, by generating control points.