Question

Does anyone know where in CKEditor I can setup, so all links added will have rel=”nofollow”, even if the users don’t specify it?

Answer 1

You can create a data filter as explained in this page that checks every link:
http://docs.cksource.com/CKEditor_3.x/Developers_Guide/Data_Processor

This (untested) code should be more or less what you need:

editor.dataProcessor.htmlFilter.addRules(
{
    elements :
    {
        a : function( element )
        {
            if ( !element.attributes.rel )
                element.attributes.rel = 'nofollow';
        }
    }
});