Yesterday, Matt Cutts of Google posted a video on YouTube named How do I know which links to remove when I get an "unnatural links" message?
Matt Cutts in the video explains basically two ways to find "unnatural links."
(1) Google more and more is sending examples of unnatural links in their unnatural link warning emails. This is rolled out and Google will give you examples of what types of links they see as being bad.
(2) If it is a recent warning, you can always see your most recent links within Google Webmaster Tools.
Here is the video:
That being said, Webmasters and SEOs are not satisfied.
They want Google to add a method of showing you which links are bad right in Webmaster Tools. They want to click on a filter to "Show Unnatural Links" only.
Is that even doable?
For the manual link penalties, probably not. Googlers are not tagging every specific link that is pointing to your site and marketing them all as unnatural. Maybe they are marking some but I can't see them marking all. Seems like an exhaustive process.
For a more automated link penalty, maybe like Penguin, I assume Google can do this. Would they? I am not sure. It can lead to spam issues if you give too much detail to those trying to manipulate the search results. But Google has been surprising me in this area, so who knows.
We do know that many people do not want this data to be public. They don't want a public site to show which links are unnatural so that anyone can tell on anyone else. But to have this data within Google Webmaster Tools, that might be useful.
Forum discussion at Twitter.