Great thread. Sadly, I don't have anything to recommend, outside of standard older, more adult oriented favorites of mine, like The Magic of Thinking Big, Think and Grow Rich, How to Win Friends And Influence People. I am planning to selectively go through these with my 12 year old son at night before bed and hope that it seeds his brain.
My son struggles with organization skills too, and is also in honors classes, very similar situation.
I'm also teaching a Personal Management merit badge class for Boy Scouts, and am trying to incorporate some of these ideas as well, and some MMM lessons as well. Looking forward to hearing suggestions too.