To which, Tedster replied that:
"The links in GWT are a much fuller list than the results returned from the link: operator, but Google never said that the GWT link list is 100% complete, and it isn't. Neither does that list filter out links that are not passing PR – whether that's because of rel="nofollow" or because of an decision Google made. When it comes to links, Google just will not tip their hand that far. "
Further, Loren baker writes that:-
"Yahoo Site Explorer also tracks inbound links using the NoFollow tag and Yahoo also says that it does not let links which use the NoFollow tag influence ranking(but it does follow nofollow links to find & index new content)."
For a better understanding about these links refer to Joost de Valk's Google Webmaster Tools External links ++.
Thread at Webmaster World.