I don't know if you guys noticed it but Kevin Goldstein came out with the organizational rankings over at Baseball Prospectus the other day. Here's the methodology:

I began by assigning points to each team for the talent it has, giving points at differing levels within the Excellent, Very Good, and Good labels used in the recently completed Top 10 lists. Additional points were granted for average prospects, as well as talent beyond their top 10 that would qualify for that level. The rankings you see here reflect the total raw points. In order to have a little fun with this, and in an attempt to provide some additional information, I then split the talent between hitting and pitching, found the average amount of hitting and pitching points, and then calculated the number of standard deviations above or below that average. Presto! Instant 20-80 scores for each category.

He lists the Yankees as having the best pitching talent in the minor leagues. Hitting talent comes in at #18 as every Yankee prospect hound would suspect. Combine the two together and the Yanks are the 4th best organization in terms of prospect talent - not too shabby.