Back story: During panda and penguin we noticed declining ranks on google. So we hit the Q&A and followed the given suggestions; removing links, optimizing a few tags, etc. We took the time and money to remove quite a few links (200+) using Remove'em. We then submitted our results to the Google web spam team (Google reconsideration request) to find out we have no manual penalty. This bring me to the thought our back links profile might still be hurting us. We had a pretty good results while removing our back links from other webmasters being very helpful and removing our links, most of which were created by old seo company's when "links were king".
This brings me to my real question, would it be worth the time disavowing links we think are bad using the disavow tool? Obviously only the ones where webmasters didnt not respond or refused to remove out link?