The link disavow tool is a way for a webmaster to state they do not vouch for a collection of inbound links to their website.
Recovering from manual link penalties will often require removing some of lower quality inbound links & disavowing other low quality links. For automated link penalties, like Penguin, using the disavow tool should be sufficient for penalty recovery, however Google still has to crawl the pages to apply disavow to the links. It still may make sense to remove some lower quality links to diminish any future risks of manual penalties. With the rise of negative SEO, publishers in spammy industries may be forced to proactively use the disavow tool.