Directhit.com, popular until AskJeeves purchased it,was well known for using click-thru data to help determine rankings. But it's gone now.
My Looksmart rep. claimed they were experimenting with it.
But worth noting, a study was done showing an increased click-thru rate on organic listings if the paid listing was also present - an argument I often use for clients who ask why do we bid on terms that we already show up for.