Alan Bleiweiss: I run them through Marie Hayne`s disavow blacklist checker. I then go through domains not identified in that report manually. You can also consider using a tool like Kerboo for that first pass work, which I also use from time to time.
Doc Sheldon: I have yet to see any tool do even a half-decent job of judging link quality. I visit every domain personally. Yeah, that makes it tough to do an audit of a site with links from 10K domains ;)