GOOGLE SAYS IT'S NOT ENOUGH JUST TO DISAVOW BAD BACKLINKS, YOU NEED TO CLEAN THEM UP
The disavow tool provided by Google is a useful option for those that may need to limit risks inherent to outside sources linking back to your website. However, while that's one important option, Google is very clear that you should make every effort to clean up bad and unnatural links pointing to your site.
"[Matt] Cutts warned that the tool should be used with caution. He also warned that publishers should first try to remove links they are concerned about pointing at them by first working with site owners hosting links or with companies they may have purchased links through."
The task of monitoring and managing the removal of inbound links can be a daunting and overwhelming task, especially for large, popular, and/or authoritative websites with important and valuable content. It may be near impossible to track and remove 1000's or even 100,000's of negative backlinks.
There is good news, however. One of Searchlight's ancillary benefits is to manage the identification of unauthorized use of content, including backlinks. Through the Searchlight claims system, each property where these bad links exist is individually tracked. A communication process begins with the goal to inform the website owner in an approachable way that the bad links should be removed. Automatic monitoring and follow up make the process of follow-through (pestering if need be) effortless.
The process of disavowing links within Google Webmaster Tools can be grueling, but also consider that Bing also has a disavow tool. When you consider that there is Bing, Yahoo, DuckDuckGo, Baidu, and so many other search engines online, it makes the most sense to make sure negative links are handled at the source.