Good answers from Philip.
The bad neighbor checker that you are using works fine. Its not 100% as you’ve seen so look at each link it targets. I also look at tools like the WOT voting tool to monitor my linking websites. Its based off of user feedback and scoring, and also lets good/bad comments to be shown.
No-follow’s say the site that is linked to is not endorsed by the linking website. Its designed for a link poster rather than a link recipient. So if you have an incoming link that you have identified as potentially having a negative effect, I would block it.
At the end of the day though I have found that once I can identify the bad links, I just firewall at the server and if you have drawn any penalty, submit the URL for reinclusion through Webmaster Central.