"Oh yes @narwhal - it can be called programmatically. In fact I use Nona.exe which does stitching by calling it directly. Its just one of the components in Hugin."

"Hmmm. well YMMV but IMHO its worth checking out the tutorials here:
http://hugin.sourceforge.net/tutorials/index.shtml These tuts are based on the early 0.7 release (2008).
It is much improved from 0.7 version and has several new robust, high…"

"You might want to also look at Hugin. It does a great job of fixing the vignetting issues between adjacent images - its also free and open source.
http://hugin.sourceforge.net/"