There's a nice article in Teaching Issues and Experiments in Ecology about how to best use the information gathered in misconception pre-tests. Basically, the author shifted from using the misconception data as a measurement of whether students were making learning gains, to using it as a tool to address the misconceptions directly.
Grant presented histograms of the results of the pre-tests in class and engaged the students in metacognitive discussion (thinking about their process of learning). He then explicitly arranged the course content around the misconceptions identified. Apparently this didn't affect the type of content addressed as much as the structure.
and also a much longer version NAS/NRC Board of Science Education here.
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