In mid-October, Google launched the disavow link tool and some have complained it doesn’t work but it seems like it does indeed work. As an FYI, it seems 50/50 have used the tool (poll over here).
Dixon Jones from Majestic SEO, a person I respect, trust and know is incredibly honest, posted in a Google+ thread that he used it for a site and it helped it get out of a manual link penalty. Dixon wrote:
When asked for more details, Dixon explained:
Now, this should work for a manual penalty fairly quickly. Those who want it to work for a Penguin link penalty need to wait for a new Penguin refresh. There is a WebmasterWorld thread just on the Penguin/Disavow topic itself.
But from this we can have a pretty good and honest opinion that the tool does indeed work and should work with Penguin if used correctly and when there is a data refresh or update.
Forum discussion at Google+.