In almost all the points made in the arguments listed in the ORG thread, there's more to be taken into consideration that any of those who posted brought into the fold.
First, let me start off by saying this: of the popular American sports, Baseball (IMHO) has been BY FAR the most unchanged over the past 40 years, in terms of rule changes, as well as perceived "eureka moments" unlocking previously unknown techniques/strategies. The baseball of today, is pretty similar to the baseball of the 30s, and almost indiscernible from the ball played in the 70s and 80s. Sure, the players LOOK different, but big burly players have always existed (Babe, Klu, etc.). I would definitely admit that, pound for pound, players are in better shape now. But, this brings me to a point that I don't think anyone has made yet.
This may come as a shock from a 22 year old, but here goes. A factor (in my mind, a major one) in trying to discern a difference between play of old and 2008 MLB is the fact that players back then gave a crap. Let me rephrase. I personally believe that the level of effort and heart exerted, NOT JUST at the major league level, but throughout a prospective ballplayer's ENTIRE existence was vastly greater and more intense in days of old, rather than currently. From what I understand, the mindset was just different back then, plain and simple. Johnny Bench sure as hell didn't have his mom's cleaning lady follow him all the way up to his private college so that little Timmy Tim didn't have to clean his own damn room. The overall mindset of youth in previous eras was BY FAR, IMHO, more conducive to a positive, driving, powerful work ethic, and the ballplayers that played in that time period were definitely affected by it.
This argument is obviously PURELY subjective, as I think any argument on this topic ultimately has to be. It's like saying that the eggs benedict that the corner diner makes is better now than it used to be, and noone can remember or prove how it used to taste! I just have to say that I honestly believe that the overall level of effort and heart exerted by players who didn't make such ludicrous (even counting inflation) salaries far outweighs any perceived or measurable advantage given to any modern player by whey protein or power bars. Charlie Hustle would be EVEN MORE dominant today than he was before, because where he excelled (the heart he put into the game) would stand in even greater contrast to the "athletes" that play today.