My article on doing digital panoramas using PTAssembler and PanoTools is now up at the Luminous Landscape photography site. If you haven't seen it before, this site is a wonderful resource for anyone interested in serious photography. I'd like to thank Michael Reichmann, the proprietor, for giving me a chance to contribute.
For some earlier entries and photos check out this, this, this and this.
As an intersting aside, the Idaho State Capitol building photo (from here) is an example of what happens if you don't set the reference image and point correctly. This is very similar to using a large amount of horizontal shift to the right.
If you have any questions on the article, let me know and I'll try to answer them here. There are a ton of resources out there on doing this stuff, so my main advice is to just jump in and give it a try.