Thoughts on using the disavow tool for removed links?

[shopbloc]

Our website has been penalized by Google for the past few months due to unnatural links. We have spent the past 2 months submitting link removal requests to the domain owners with success. However, the Google Webmaster Tools "links to site" has not updated the list. I understand that they update the list of links as they crawl the website, but it has been 6-8 weeks on a lot of them (mostly our biggest offenders). We attempted to send a reconsideration request anyways, hoping Google would see that even though it is still listed, the link isn't actually there.

We received a response that it is still in violation, but I believe it is because the webmaster tools links have not updated and perhaps this is what they go off of. Would you recommend submitting these domains to the disavow tool even though our link has already been removed for the past 6-8 weeks? Or even just listing them with the "#" comment tag so they can see they had been removed? Or would you continue waiting for it to update? Of course, we would like the penalty removed as soon as possible and were concerned that the list hadn't removed these websites the past 6-8 weeks our link had been removed.

Example: This domain shows we have 3,397 within this website. It was an affiliate that had this URL forwarding to our pages: http://www.binet.lv/go.pl?PID=49276714O2422 . This no longer forwards to our webpage and the affiliate has been expired, but the GWT still shows them at the top of the links list.

I also noticed a lot of sites left the links up, but added the nofollow attribute. These are still coming up in the Links list and does not decipher between which do and do not have nofollow. Could the spammy sites with our links as nofollow still be hurting us?

Thanks for any help and recommendations!

[DarinPirkey]

The disavow tool is something I would use cautiously!  Continue to do the same practices you are currently using (contact the webmasters) and make sure that you are adding quality links going forward.  I have a client that had the same issue and we got our rankings back (though not all the way) by contacting webmasters and creating a positive link structure with all of their new links.  (they were doing a lot of "blackhat" stuff before they dropped and called us)

If you do decide to use the disavow tool, I would check out this great article by DeJanSEO that they posted back in October (http://dejanseo.com.au/google-link-disavow-complete-guide/)

Let me be clear and say that I'm not saying that every link you want to be removed should go on the disavow document.  It should only be used for those excessively spammy links and where you've tried to contact the webmasters and have had no success.  You can write notes to Google in your document that tells them the efforts you have made to remove the links.  They do actually take that into consideration and if you provide more positive links going forward, that should do the trick.

[shopbloc]

Yes, I agree that the disavow tool should be used as the last case scenario. I am more frustrated that Google is still stating that we are in violation of their guidelines due to unnatural links. But most of the major offenders have removed them and it is still showing up on my Google webmaster tools. I am assuming this is what they look at when determining if we are or aren't.

How long does it take for GWT to update? Our links have been removed for about 4-6 weeks, but they are still showing up on "Links to your site".

Thank you for your time and help! The link reference you gave was very helpful.

[DarinPirkey]

Take a look at these two videos from Google for reconsideration

http://support.google.com/webmasters/bin/answer.py?hl=en&answer=35843

http://www.youtube.com/watch?v=cA5I3HHApYk

These talk about the reconsideration process and some best practices.