We engaged the services of a 3rd party SEO consultant to assist us in managing our Meta data and to write regular blogs on our site http://cyberdesignworks.com.au Without our authorisation, the SEO also ran a link building campaign which has seen us Penguin slapped and we no longer appear in Google for a number of our core keywords.Since notification by Google that we have unnatural links back in March we have undertaken a significant campaign to rid ourselves of these dodgy backlinks by a number of methods. I have just received feedback on my 4th or 5th resubmission which is still advising that we need to make a substantial, good-faith effort to remove the links before Google will reconsider us for inclusion. After the effort that I have gone through to get links removed, I am now at a loss as to what else I can do to demonstrate substantial, good-faith effort to remove the links.Below is a summary of the actions that we have taken to date.According to http://removeem.com we had about 5584 back-linking domains.Of those we have successfully contacted and had removed links from 344 domainsWe ignored links from 625 domains as they were either legitimate press releases, natural backlinks or client websites containing an attribution link in the footer that points back to us.Due to our efforts, or the sites simply becoming defunct, removem.com reports that links from 3262 domains have been removed.We have contacted but are yet to receive feedback from 1666 domains so we can assume that the backlinks remain.We have configured an automatic 301 redirect for each of the links from these 1666 domains to point to http://redirects.sanscode.com/ which we are calling our Bad Link Catcher (a stroke of genius I thought). i.e http://www.mysimplewebdesign.com/create-a-perfect-webpage-with-four-important-tips-from-sydney-web-development-service-companies.php As we are a web design agency, we have a large number of client websites which contain an attribution link in their footer which points back to us. We have gone through the vast majority of these and updated these links to replace anchor text with an image and rel=nofollow link. i.e <a rel=nofollow target=_blank href=http://www.cyberdesignworks.com.au/><img src=https://sessions.sanscode.com/site/assets/media/badges/Badge_CDW_SANSCODE.png></a>See http://www.milkatwork.com.au/An export from http://removeem.com detailing the number of times we have contacted each link and whether it is still found or not was also supplied with each resubmission.The total back links reported in Google Web Master Tools has dropped from over 100K to 87K and I expect it to drop significantly lower once Google re-crawls each back-linking page.Based on all of the above, I am not sure what else I can do to to demonstrate a substantial, good-faith effort to remove the links.I would sincerely appreciate any feedback or suggestions that you may have as I am out of ideas. 
What constitutes a substantial, good-faith effort to remove the links
google search console;301 redirect;seo audit
The Penguin update penalises sites that have a high proportion of unnatural inbound links. One thing that constitutes unnatural inbound links is identical anchor text used in a high proportion of those links.In this report from Open Site Explorer for your URL, there are 22,735 links containing the anchor text sydney web design. Proportionally, these appear to make up the vast majority of your inbound links. It's possible that this is the reason you've been penalised.Open Site Explorer reports that those 22,735 links are spread across 48 root domains. (You can discover some of them by clicking the plus sign to the left of the sydney web design text.)I would suggest focussing your efforts on these 48 domains to ask them to remove this text and reduce inbound links with that term to a level that's proportional to your other inbound terms. If you've already contacted some of these webmasters, persevere without being rude about it and see where it takes you. If you've already removed links on these pages, it might take time for the changes to take effect.My experience is that when Google says things like substantial, good-faith effort to remove the links this is simply a nice way of saying we want to see those links gone. They're probably not too interested in the effort you expend getting rid of the links; they're more interested in them disappearing altogether.Finally, I would petition your SEO consultant to help you with the clean up if you can. This stuff is time consuming, and it sounds like it's not your fault that you've ended up in this position.UPDATE 17 October 2012Google have just launched their disavow links tool which lets you clean up backlinks by telling Google which incoming links you'd like them to ignore. I'd recommend that you use it to ignore any backlinks with boilerplate text that you feel may still be affecting your rankings.Matt Cutts has a video on YouTube with more information. He says that disavowed links may take weeks to update, so it's probably worth waiting a few weeks before you ask to be re-included.