Thanks all. I just use the Photostitch support that comes with the Canon camera. It allows you to see the previous pic while you are taking the next pic so that you can line them up. Then, I use the Canon Photostitch software that comes bundled with the Powershot S40 and merge them.
Here are a couple more (non-reef related) stitches. First is a 2x2. Notice the curved horizon. Wasn't intentional. Just the way I took the pics. If I use a tripod, I would get better results.
construction
Next one is horizontally stitched (6 images I think) and resized significantly for webviewing.
vancouver panoramic
Check out this one of Key Arena. Notice that a couple of men walking down the stairs on the left can be seen twice in the pic?
Key Arena