I have used a program called "The Panorama Factory" with pretty good success. There are some times when it can't blend the photos to an acceptable quality (usually due to my hand-holding the camera). I have also used PT Gui, but it is very time consuming, with great results.  I agree with shooting full manual, and use a tripod if it is a planned shoot.

Here is some additional info:

http://www.luminous-landscape.com/tutorials/digital-panoramas.shtml

http://www.tawbaware.com/maxlyons/index.html

Matt