Link disavowel is desired someone (a competitor, or simply a derranged troll) has created low-quality links to your site. In some cases, in competitive, global markets, this may actually be the result of perhaps hundreds of domains created for the purpose of wrecking large numbers of competitors by providing Google with evidence of negative behavior. Since things things are sorted algorithmically, and Google's current algorithms might not have the more global perspective needed to see such a problem, it is incumbent that people with websites need to monitor what links are being created to those sites.
Google Link Disavow Tool
What this means in practice is, a part of managing a site is to monitor inbound links and take action when necessary. There are two tools to do this: - Regularly monitor inbound links as reported in Google Webmaster tools - Google Webmaster Tools > Search Traffic > Links to Your Site - Use the Google Disavow Links tool to ensure that any poor quality links are disregarded by Google. > Remember, Google (and Yandex) treat https://domain.com and http://domain.com as different properties, and so even if one is using 301s to route to a primary domain, any inbound domain will need to have its links dealt with at the level of its original domain protocol. This means registering both http:// and https:// versions of a site, and possibly www for each as well (resulting in 4 different property configurations of a single site site, when using 301 redirection).
Google Link Disavow File
Each property in Google Webmaster can have a single Link Disavow text file. In that file there can be links and/or domains that are disavowed. In many cases, especially if poor quality links are regularly being created in an ongoing blackhat campaign against a site, domains will be used over and over to get a count of several links from each poor-quality site to the target site. It is easier to manage with a list of domains than a longer list of each link.
Bing Link Disavow Tool
The Bing Webmaster Disavow tool is a lot less flexible (they require manual entry one-at-a-time for each domain/link, see complaint):
Yandex Link Disavow Tool
Unfortunately, there appears to be no way to disavow links in Yandex Webmaster tools (an otherwise useful set of tools). There is no Yandex Link Disavow tool. As of 2015 Yandex was stating that they had no intention of creating such a tool.
Disavow Files Crowdsource Tool
Bruce Clay crated a crowdsourcing site for disavow files, which has a decent dashboard, but not much functionality beyond basic reporting (the idea is that all disavow files are parsed and any new inbound links matching previously reported files/domains would create a notification for the user).