It's all the engineers, I think.
Football Outsiders finished their work on the most "efficient" offenses and defenses of 2008 and they have good things to say about Penn State.
Before the numbers, a quick precursor:
Game Efficiency quantifies the success rate of a team scoring while in possession of the ball and preventing scores while not in possession of the ball over the competitive course of a game.
It's a measure of how well a team takes advantage of their drives. It's not measured on a play-by-play basis, but rather what a team does with each possession (and how well they defend their opponents' possessions).
They go on to point out that garbage time is excluded (something that isn't a perfect science). Offense and defense are them combined into something called the Fremeau Efficiency Index (FEI). This is an SOS adjusted number, more about that in the link above.
The 2008 results?
The concept it similar to one that basketball has rapidly adapted, putting gross stats in context of game situations and possessions. The number of yards a player gains isn't very insightful if you don't know how many times they touched the ball. In that same way, team stats need context as well.
As for Penn State, their high rank in this compilation category is a result of incredible balance: Clark's TD/Int ratio (3rd in the BT) and QB Rating (24th nationally, 1st in the BT), Royster's yards per attempt (18th nationally, 2nd in the BT) and Kelly's FG% (83% overall, perfect inside of the 40).
On the defensive side, the traditional stats tell the same story. Penn State was top 10 nationally in all of the following defensive categories: total yards, rushing yards, yards/game, tds, points/game, sacks and interceptions.
Bottom line: Penn State appears to have earned their 11-2 record, and the improvement from Alamo to Rose wasn't a drastic change in turnover margin or special teams plays, but rather an almost universal upgrade in core football skills. It's something to keep in mind as we start previewing the 2009 season.
For interest's sake, other notable teams in the three-digit bottom of the 120 teams ranked: 102 Toledo (fired their coach even after a win at Michigan) and 106 Indiana (and they are actually worse at basketball).
Stats from statsheet.com