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.