Google has put out a new Webmaster Help video discussing the Disavow Links tool, and whether or not it's a good idea to use it even when you don't have a manual action against your website...
Google's Matt Cutts takes on the following question:
Should webmasters use the disavow tool, even if it is believed that no penalty has been applied? For example, if we believe 'negative SEO' has been attempted, or spammy sites we have contacted have not removed links.