With my own experience, I have found that the rule of thirds does apply to panoramas.
See here:
Larger version here Warning: HUGE PICTURE, 9.4 MB
or
here (50 Kb)
This picture has two spots where the rule of thirds is in effect: the silhouette of the foreground are at the bottom third and the mountains peaks to the right are located around the top third.
In regards to your picture Clockdoc, I think the crop with the horizon line at the bottom third is the best for your image, it draws the eyes to the boats and balances nicely with the larger sky.