We have made some links nofollow in recent weeks, but they are still showing up in Google Webmaster Tools. Does GWT ignore these links? Will they vanish as the index is updated, or do even nofollow links show up here?
Simple answer: Yes, GWT shows all links, followed and nofollowed.
Actually Google Webmaster shows all the links whether it's dofollow or nofollow. But it does not pass link juice from a nofollow backlink. I am also doing SEO for a company and when I look at their backlinks in Google Webmaster tool I see lots of Nofollow links that are pointing to them.
No! Google Webmaster Tool only shows all the links pointing to your website but not showing all the do follow and no follow attributes..