Lots of good advice on this thread. Here is a short blog entry about panoramic projections: http://www.trailpixie.net/photography/comparing_focal.htm
Some general comments:
1) Several folks have said that you need to shoot in manual mode and lock the focus. This is good advice for many circumstances, but you can stitch images at different exposures....and you may even want to do that if there is lots of dynamic range. When you use this technique, make sure to increase overlap.
2) Two techniques to help you take rapid fire panos:
[blockquote]A. Shoot raw (always a given for me) and then use the exposure lock button to rapidly make a pano without the effort of changing modes. The exposure lock button allows you to set the exposure to one setting across multiple exposures.
B. I also have mapped the focus function to the AF button on the back of my canon. This allows me to focus on a single focal point of the pano, then recompose and set exposure (see above). By keeping my finger off the button for the duration of the multiple frames, I don't have the camera refocus. [/blockquote]
3) I frequently process my raw files differently to provide the illusion that the light level is remaining somewhat constant. I set the white balance and exposure for all the images, then work back across those that are either too dark or too light to shift them subtly towards the exposure I wanted from my key image.
4) When you shoot panos, remember to note the starting angle on your panning clamp. I can't count the number of times I have failed to do enough exposures on the second row. http://www.trailpixie.net/panoramics_go_b.htm
5) When shooting water scenes, try to get stationary objects that can be used as control points into every frame. If this is impossible, manually create the control points and guess about their location. You may need to do some manual blending later.
6) Partly cloudy, breezy days are the bane of the panoramic photographer's existence.