Andy_Langton - 8:13 pm on Feb 28, 2013 (gmt 0)
A few things here.
As netmeg suggests, the GWT report is woefully inadequate. But Google themselves have suggested that these are the links to address when looking at reconsideration/disavow. I am totally confident that the GWT report does not show all of the links that Google evaluates. This is a bit of a mystery to me. Is it that they won't count the links not shown in GWT against you? Is it that the statement simply isn't true. My best guess is that as far as manual action is concerned, GWT may be sufficient. But from what I've seen, many manual actions for links are accompanied by algorithmic penalties anyway.
The second thing is that Google have (somewhat paternalistically) suggested that you must remove links rather than just disavow them all as some sort of show of 'good faith'. Again, this is a little difficult to put into precise terms.
According to Matt Cutts at some point in the near future they are going to give us examples in GWT of links they consider not natural. Maybe wait until then to see what it shows.
I wouldn't wait for that, to be honest. Any examples from Google are likely to be highly obvious.