A little behind the New York Times (You Paid How Much for That Bike? in November ‘06, now behind their ridiculous paywall), the L.A. Times takes a look at custom high-end road bikes, interviewing Rob Vandermark of Seven Cycles and Lennard Zinn.
There’s also a good summary of traditional road bike fitting conventional wisdom: Knees over pedal spindle, handlebar flat obscuring the front hub, with balls of your feet directly over the pedal axle and your feet parallel to the top tube. Pain in the front of your knee means your seat is too low, while pain in the back of your knee means you’ve cranked it up too high.
Those are all good rules of thumb, but keep in mind that different physiology may require different positioning; if any of those rules don’t work for you, talk to an experienced bike fitter at a shop.