Our external links just dropped like 70% in GWT for our 2 year average. On a side note GWT reports the last time it asked for our robots.txt was July 24th yet parsing the raw log shows 30 or 40 googlebot requests for the robots.txt since then.
After 3 or 4 post I have made here and great responses from Tedster which calmed my oh so paranoid mind I have come to the conclusion that GWT data is nice to look at but means just about nothing.
As Tedster always told me, do you see a drop in traffic? No? Then dont waste your time trying to figure it out. :)