ZydoSEO - 1:36 am on Nov 13, 2012 (gmt 0)

The typical notice reads as follows:

We've detected that some of the links pointing to your site are using techniques outside Google's Webmaster Guidelines. 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 have any questions, please visit our Webmaster Help Forum.

The sentence that I've bolded/italicized tells you that your site is not being filtered or penalized as a result. I read it as saying, essentially, that they have flagged the links they believe to be "artificial or unnatural" to be ignored by their algorithm.

Of course, they would love for you to also get those links taken down so that it reduces the workload on their end. Thus the subsequent comment, "If you are able to remove any of the links..."

I'm thankful...

a) they actually send out messages about such issues now and
b) they actually respond after they have processed a reconsideration request.

Not so long ago, you never received ANY information/response from them.