To add to Rod's answer: PDF output will create an interactive PDF, the SWF is embedded in the PDF. When playing the PDF with Adobe Reader (that has the special embedded Flash player) the user gets the same experience as when playing a SWF-output file. This is a good option for users that don't have access to Internet. However since some versions, Adobe Reader is not installed by default with that embedded Flash player, which spoils the game of course.
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