I just wanted to add to this discussion to say that I created a tool that helps me create really good spreadsheets for link auditing. It aggregates links from a number of sources, reduces the list down to one link from each domain, and marks the nofollows. It also tells you which links are from domains that are on my blacklist of domains that I almost always disavow. The blacklist contains over 14,000 domains at this point and is growing. And, it tells you which links are from domains that I usually ignore such as dmoz scrapers and domain stats pages where we know the link is not one made for SEO purposes.
I'm not a fan of tools that automate the decision making promises because I've seen so many of them mark fantastic links as bad ones and miss a whole bunch of really spammy links. If you're trying to escape Penguin, you have to be way more accurate than this.
It's still in a beta phase right now as I am working on making it as useful as possible, but you can see the details here: http://www.hiswebmarketing.com/manual-link-audits/