Link Removal Guide

Back in 2012 a lot changed in link building, and for many the first step is now to undo the work previously done which starts with finding the low quality links that may have been built many years ago, especially if you’ve been hit by a penalty. There are 2 types of spam penalties applied to a website: a) site-wide matches action that impact an entire website, and b) partial matches which impact individual URLs.
Google is willing to take manual action to remove spam:

Wondering why did you get a spam penalty? A good answer could be to stop trying to game the system and start delivering quality. Link schemes, link exchange, link networks, article marketing, press releases with money keywords in anchor text.. it’s time for action in order to lift the penalty.
Below I’m describing in brief the link removal process, kind of a link removal guide, which includes:
1) link discovery from multiple sources
3) manually auditing each link by quality, authority and relevance
4) contacting webmasters to request link removal
5) submitting a disavow file for none responding webmasters
6) submitting the reconsideration request
I usually start looking for bad links in the “Links to Your Site” feature in Google Webmaster Tools a good place to start the investigation. Below is a also list of tools that helps you grab your links from:

Links API extension for Excel – to grab link metrics from Open Site Explorer and Majestic and SEO tools for Excel to grab the HTTP statuscode and PageRank.
Check on Webmaster Tools for links that were flagged inactive in other sources, if it reports them then add these to your final disavow list.
Auditing the backlinks, there are link audit tools like LinkDetox, cognitiveSEO, Rmoov.. which claim to audit links for you by grading them, but it is well-known already that nothing beats a manual link by link check.
Then the email outreach, Rmoov does a good job of gathering domain contact details and scheduling emails out to webmasters on your behalf but a lot of imprint pages have the contact details in .jpg format, not sure if Rmoov can help in this situation..
Write an effective link removal request by keeping it short and specific, to avoid the recipients spam folder.
Place your spreadsheet contents of all links removed in a Google doc, screenshots with contact forms, source-code for emails sent.

When you’re done with all the work to understand what bad links your site has, and worked to try to get as many removed as possible, then that’s a good time to use the disavow tool, to disavow any that remain. Remember this is only for one single domain, if you want to disavow links from multiple domains then you’ll need to add an entry for each domain.
Google currently support one disavowal file per site (file size limit is 2MB) shared among site owners in Webmaster Tools.
If you want to update the file, you’ll need to download the existing file, modify it, and upload the new one.
The procedure you need to follow, involves creating first a simple .txt file and then uploading it. The format for the file is to add a line for every link or domain you want to disavow.
# at the start of a line means a comment for Google
I usually submit TLDs (top level domains) in the disavow file and not each specific link.
There is also a helpful tool in this direction, from Geekiti:
6 most common mistakes made when using the disavow tool:

And in the end, the message from Matt Cutts, Head of Google’s Webspam Team, is don’t bother playing tricks with your disavow files:

The reconsideration request, if there is a manual action in place then you’ll see “Request a Review” button on Google Webmasters Tools, which will let you access the reconsideration request form, where you’ll have to write it.
You’ll have to mention any violations of Google’s quality guidelines that were happening on your site, who did it, and what you have done to repair the situation.
Provide a link to a Google doc that includes dates contacted, email addresses and contact form URLs used, text content of email sent, responses and results.
Describe briefly your future plans with the site and make it clear that you understand what is expected, assure that you’ll not violate their quality guidelines again, and very important: request that Google reconsider the way your site is indexed.
Learn more about Google reconsideration request from Matt Cutts:

Within 30 days of submitting your reconsideration request you should be welcomed in Google Webmasters Tools with “Manual Spam Action Revoked”.
Good luck out there!