Over the past month or so I have received a lot of emails from people begging me to remove their links from my blogs because they believe they are the cause for their recent drop in Google's SERPs. Half of the links I've been asked to remove are from my top commentator plugin. Is this just people panicking or does having your link in a top commentator plugin hurt you in Google's SERPS sincde the recent updates? I've searched a little bit online and from what I can read it only seems to hurt me (increase in spam, giving away PR because my blogs are dofollow, etc)
Well, I do not believe that this could hurt someone's ranking in Google, but you can always add rel="nofollow" to all links inside the list.
Yes it would, lets say site A has top comments plugin, it links to site B. But if site A has lot of junk links coming to it then it will indirectly affect site B
Links do not affect sites unless there are really lots of them and all of them are unnatural + placed on spammy/unrelated sites (that's something what Matt Cutts said).