For general directories that we never asked to be listed on... is it a good idea to use the disavow tool for these types of links even if we haven't received any kind of penalty from Google?
The author of this article (http://searchenginewatch.com/article/2260344/Racing-Penguin-How-to-Attack-Unnatural-Links-Before-Penguin-Hits-Case-Study) seems to think so... assuming your efforts to remove the link fail.
Thanks for letting me know about using this tool, it was really helpful to me, there is no doubt to it, really.
This tool can help in putting no credit to links or simply telling Google not to count the links as votes for the sites.
I would never use it if you haven't got a penalty. My gut feeling is Google knows about those auto-scraper sites way more it does about link networks (which could be something to worry about).
By the way, here is a nice post about how to tell if you need to use the disavow tool at all http://www.link-assistant.com/blog/the-professional-link-audit-before-disavow/