If bad links are now ignored why bother to resubmit a reconsideration letter?

[SEOEnthusiast]

So what I don't get is that Google says it will not trust and ignore these Spam type links so you lose only the value from those specific links.So if someone was hit with a penalty why should you bother to write a reconsideration letter if Google is supposedly just ignoring the value of the poor links anyway?

On the other hand in their message they do state if you are able to remove any of the links you can resubmit --- this is sending conflicting messages.

Back in the day you get your entire site hurt, now it seems like it can potentially just be a few keywords or pages.Does it make sense with the new roll out  in March 2013 to still do a reconsideration request?

[SEOEnthusiast]

So what about links that show a high number of links (hundreds or thousands) but are quality websites. Do I disavow all those links just because they have a lot of links pointing to my site?

[MarieHaynes]

A lot of people who do penalty work will recommend that you use other sources outside of WMT such as ahrefs, OSE and majestic.  However, I only use WMT and it seems to work for me.

I think that the reason why people recommended to use the other sources is that in the past, WMT really only gave you a tiny sample of your links.  This has changed though.  Also, John Mueller said a while back in a WMF question that for most sites, using just the links in WMT really should be enough.

[SEOEnthusiast]

So then for links to remove do you think it should only be links that are found in Google Webmaster Tools?

As I could have many links outside of GWT is it possible all 'spam links' they have ignored and I won't find in GWT or are they All there and should only consider removing links from here since this is what they see

[MarieHaynes]

Did you get a message in your WMT?  Some people lately have been getting the different type of unnatural links warning that says,

"We don’t want to put any trust in links that are artificial or unnatural. We recommend removing any unnatural links to your site. However, we do realize that some links are outside of your control. As a result, for this specific incident we are taking very targeted action on the unnatural links instead of your site as a whole. If you are able to remove any of the links, please submit a reconsideration request, including the actions that you took."

If you got this warning, and if there is no yellow caution symbol next to it in WMT AND you have not seen a drop in rankings then yes, you are correct that you can just ignore those unnatural links as Google has granularly discounted them.

The regular unnatural links message is:

"We’ve detected that some of your site’s pages may be using techniques that are outside Google’s Webmaster Guidelines.

Specifically, look for possibly artificial or unnatural links pointing to your site that could be intended to manipulate PageRank. Examples of unnatural linking could include buying links to pass PageRank or participating in link schemes.

We encourage you to make changes to your site so that it meets our quality guidelines. Once you’ve made these changes, please submit your site for reconsideration in Google’s search results.

If you find unnatural links to your site that you are unable to control or remove, please provide the details in your reconsideration request."

If you got that warning, OR if you got the first warning and you ARE seeing a ranking/traffic drop then, yes, you need to file for reconsideration.  If you don't then your site will remain penalized and will have trouble ranking for some or all keywords.

[mememax]

Hi Nevil, first of all Google WAS ignoring the low value links pointing to your site. In the past having a link was always worthwhile. The least value they may pass was 0. Actually links may pass negative value to your site and the general consensus is if the ratio of those links pointing to your site is superior to a certain threshold (about 70% although portent says it would be 50% in the future) your entire site will be considered low value and "penalized".

Also there may be the case you were buying links. Google doesn't like people trying to game their algo so you want to get away from leaving patterns which may lead google to think you may have done this. If so you'll be probably negatively flagged.

About the reconsideration request it only have effect if your site received a manual penalty from google which normally confirm that with a message in your webmaster tools of unnatural links pointing to your website. In this case you want to send google a proof that you're really trying to change the way you build your links and tried to clean every sign of bad behaviour using all the tools you have, both contacting those sites to remove low value links and if not possible to disavow them.

This is to simplify a lot a widely more complicated scenario where many factors can act. Also you may be affected by Panda (as you said a number of low value pages are dragging your site down in rankings) in this case you want to get rid or improve those pages, but when this comes to links is a Penguin matter. People tries to get rid of bad links just becasue if Penguin hits you you'll need to wait until the next release (and they update very few times by now) until your site will see the light again.

Hope this helps clarify your doubts.