A Google Webmaster Help thread has one webmaster convinced that links are hurting specific pages or sections of his site from ranking well in Google. Yes, he wants to disavow the links but Google's tool is not yet live.
Google's John Mueller said that if you have bad links you know are hurting your ranking, you can 404 page not found the page, remove the page the links are pointed at and Google will disavow those links.
John explained that you can even move a whole subdirectory to a new subdirectory if you feel the subdirectory was hurt by links and you can remove those links. John added that most of the time, Google won't penalize a site for bad links, and Google does a good job of ignoring the links. So going this 404 route is a step most webmasters probably shouldn't do.
Here is what John had to say:
In general, if you remove the page that is being linked to (such as a spammy forum thread) and make sure that it returns a 404/410 HTTP response code, we'll ignore the links to those pages. If these links are primarily pointing at threads that you've removed, then there's no need to move the whole forum to a new URL. If you find that there's a significant number of problematic links that you can't remove which are linking to general parts of your forum (eg the forum homepage), moving the forum to a different URL might be a possibility (but I'd only recommend doing that if you're absolutely sure that these links are causing problems -- we're pretty good at ignoring spammy links). If you choose to move the forum, then StevieD has some good suggestions on how that could be done (make sure that your 404 page is useful to users too).
This is not exactly new, John said links to a 404 page won't hurt you but this is the first time he went into the topic in such detail. At least as far as I know.
Personally I think, this is an extreme measure and 95% of webmasters probably should not do this.
Forum discussion at Google Webmaster Help.
Image credit to BigStockPhoto for 404 image
