I believe that in Eclipse, the only kind of exclusions you can specify are things like "exclude all protected members" and package-based exclusions (not class-based exclusions.)
If you're using Ant to generate them, you can use the nested "package" element, and you can use a fileset nested element and add exclusions to that fileset.
For example:
<javadoc >
<sourcefiles>
<fileset dir="${src}">
<include name="**/*.java"/>
<exclude name="**/ClassToExclude.java"/>
</fileset>
</sourcefiles>
<packageset>
<dirset dir="${src}">
<include name="com.mydomain.*"/>
<exclude name="com.mydomain.excludePackage"/>
</dirset>
</packageset>
</javadoc>
P.S. - I've used the <sourcefiles>
element alot, but never the <packageset>
element. The latter might not be spot-on syntactically.