I'll be honest, I am still confused on this. The other day, I reported on how an ex-Googler who worked in the web spam team, said that every manual action must be acted on or else the site will soon be penalized and have a negative ranking applied to it.
I honestly thought before I wrote that post that some manual actions do not lead to negative rankings. I wrote, "I tried to look back at an example of a manual action notification that I thought did not impact the site, but maybe..."
So then I spotted this comment in a Google+ thread from Google's John Mueller not saying that. He said:
That generally means that we're not counting some of those links in the way that we might have in the past. If you're aware of specifics around those links, then I'd recommend resolving them at the source and doing a reconsideration request. If you're not aware of the specifics, remember that we're essentially ignoring those links, so the rest of your site, and the other natural links, will be used as before. In short, you don't need to take action, but if you're aware of specifics, it's always good to clean up the issues directly too.
I bolded the "you don't need to take action" part, because you don't.
So we have a Googler and an ex-Googler suggesting two different things. So John came back in and said, "I'd recommend watching Matt's video on that specific type of manual action, he covers some corner-cases that make things a bit clearer."
So it seems John is implying that Kaspar is not wrong, because he is referencing corner-cases. However, I cannot find that specific video with the corner-case mention.
In short, it seems clearly that not ALL manual web spam notifications require an action from a webmaster. Meaning, not all notifications related to web spam are negatively impacting your site.
Or maybe, Google isn't counting some links, so removing the links won't have a negative or positive impact anyway.
See, I am confused.
Here is the video, it isn't 100% clear what to do here: