Kevin GoldStein of Baseball Prospectus annual Future Shock segment has been ranking each MLB team by quality of prospects. For 2011/2012 I have, with the help of a few intrepid data input fiends at Orioles Hangout, compiled the rankings and assigned a total score to each team. The math is simple, tally up the total number of stars assigned by Goldstein. Weighing the 5 and 4 star prospects more heavily might be wise, but for now, its this is simple.
Goldstein is only ranking each organizations top 11 (plus the next 9), assigning stars for quality. 5 stars is the highest, 2 the lowest. Everyone else in the top 20 is more a less a 1 star prospect, but that doesn't show up in this ranking. These scores are only for the top 11 who get 2, 3, 4, or 5 stars each.