I've been meaning to mention this for a couple of weeks, but better late than never.
Have you tried our very own Penguin Backlink Analysis and Disavow Tool?
It's free! (at least for now)
Even better, it's really good!
Here are some screenshots (had to blur out a lot of data to protect client info).
There's more that I haven't shown, but this should at least give you an idea of the type of info given.
Basically, you just upload the backlinks given in your Webmaster Tools and let the tool run the analysis. Of course, once you get the report listing Live Backlinks, Dead Backlinks, and a summary, you have the job of deciding the value of them all. So, it still takes a lot of manual work, but the tool helpfully provides links to Whois, Majestic, Wayback Machine and more to help you determine the value of each link.
The two checkboxes (Root and URL) let you choose which links should go into a disavow file, and then creates the file for you.
Love the tool! It was just one of many that I used for this particular client, but it was definitely useful. Just thought I should point it out in case anyone had overlooked it, among all the free tools we have here.