How can I add rel=”nofollow” attributes on RSS widgets?

There seems to be no way to do that. You could filter 'clean_url' (like I did here), but I don’t see a simple way to deactivate the filter when the RSS widget is rendered.

You could open a ticket on Trac and ask for a filter in wp_widget_rss_output() … from my experience wasted time, but there is no third option.