kchacker well, when the guy that wrote a 5 (was it 5?) page article about it says he doesn't align his, I think I'm close to the truth. If you read that article, it's obvious that no one really knows what's going on. All they do is theorize and hope they're right.
The take a club they can't hit, spin it around until it vibrates like they like, then put it together. They go back out with it and hit it better because they think it's better and they believe they're on to something.
Simple fact is, I bet any of the top 10 golfers in the world could take my clubs and shoot even par with them. They're probably a solid 2 flexes too soft for them, none are "aligned", and the grip size is probably bigger than they like. Quite simply, the most important part of where the ball goes when you hit it is NOT whether the shaft is "aligned". The most important variable is the swing. As has been said before, practice more and you will score much lower than if you spend that time spinning your shafts around to some arbitrarily determined point.