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 site.
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.
As Cutts notes, the main purpose of the tool is for when you've done some "bad SEO" yourself, or someone has on your behalf.
"At the same time, if you're at all worried about someone trying to do negative SEO or it looks like there's some weird bot that's building up a bunch of links to your site, and you have no idea where it came from, that's a perfect time to use Disavow as well."
"I wouldn't worrying about going ahead and disavowing links even if you don't have a message in your webmaster console. So if you have done the work to keep an active look on your backlinks, and you see something strange going on, you don't have to wait around. Feel free to just preemptively say, 'This is a weird domain. I have nothing to do with it. I don't know what this particular bot is doing in terms of making links.' Just feel free to go ahead and do disavows, even on a domain level."
As Cutts has said in the past, feel free to use the tool "like a machete".