How to exclude classes from being documented by ASDoc 3.0.0?

The best way seems to be to exclude all classes from included SWC libraries, as shown in “How to set up ASDoc in Flex Builder“.

For release builds of your Flex project, you may import source classes instead of including SWC libraries, to minimize the SWF file size. For this, simply delete the the SWC library entry in the project properties, and instead add a source path to the sources that made up the removed SWC.