All low-quality links affect your SEO, whether they come from comment spam, pingbacks, or sites you don’t want to be linked to. Until now, to make them disappear, it was necessary to operate manually at the will of the sites concerned, which means mission impossible in many cases.
You can then send a file that declares the different links that you want to see disappear from your referencing map:
The text file will be of the format:
# Contacted owner of spamdomain1.com on 7/1/2012 to
# ask for link removal but got no response
# Owner of spamdomain2.com removed most links, but missed these
The #s precede a comment that will not be interpreted by Google. If you want to exclude a full domain, the command to indicate is “domain: spamdomain1.com” will suffice, to exclude a particular page, the url of the page will suffice: http://www.spamdomain2.com/contentA.html
Here are some explanations given directly by Matt Cutts.