I whipped this up pretty quick using the filter code from Six Apart's rel=nofollow spam catching plugin.
Here's the link to the plugin: http://www.phaedo.cx/includes/wpNofollow.php.zip
The source: http://phaedo.cx/includes/wpNofollow.phps
It basically just filters anchor tags and adds in the rel=nofollow attribute. Google, MSN, and Yahoo! all announced support today for this tag. You can read more about it here: http://phaedo.cx/archives/2005/01/18/support-for-nofollow/ there are links to everyone's announcements.
The comment text filtering is automatic, but if you want comment_author_link to return a link with the attribute in it, you need to replace the call to that function in wp-comments.php with the function in my script named comment_author_link_nofollow().
this is my first plugin for WP and I'm sure I've not done everything 100% correct, so please feel free to comment and criticize, I can take it :)