ok I understand that because of Penguin some or the links which were counting before are not counting now. But I am more concerned with the links that still show in GWT that could potentially be harmful.
To give examples, I have links showing from:
If you visit those sites you will see that they are poor quality and not related to my industry.
The links are no longer there, but according to GWT they are.
Perhaps Google has discounted them anyway but I have no way of knowing whether they have or have not but they are not sites that I wish to be associated with and they could be considered to be "bad neighbourhoods".