Gelf Magazine enlisted the help of ZEUS, a football game analyzing computer, to see which NFL coaches called the worst plays at critical times during the 2007 season.
On average, suboptimal play-calling decisions cost each team .85 wins over the course of the season.
In particular, the world champion Giants should have won another game had they called the right plays at the right times. ZEUS also analyzed play calling in "hyper-critical" situations (those fourth-down decisions with five or fewer yards needed for the first down) and found that on average, teams made the wrong calls more than 50% of the time. Here's an interview on the results with the guys behind ZEUS.