Three ways:
1) http://java.sun.com/j2se/javadoc/faq.html#recursesource
This has a java program that collects package names, which
you then pass into javadoc.
2) Another posting in Javadoc forum states this can be done with Ant.
I have not tried this.
3) Wait for Javadoc 1.3 Beta 2, available this fall.
It has the feature -subpackages that does exactly what you want.
-Doug Kramer
Javadoc team