Interesting study conducted by Scott McKinney of the Royals Review Blog.
He looked at Baseball America's Top 100 Prospects rankings from 1990 through 2003, and calculated eack player's ultimate WAR contribution during their club control years.
He found that Baseball America had a good track record with prospects, but the failure rate was very high, especially for pitchers.
Keeping in mind these are the top rated prospects in all of baseball each year, it kind of puts a realistic view on farm systems and their success:
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About 70% of Baseball America top 100 prospects fail
•Position player prospects succeed much more often than pitching prospects
•About 60% of position players and 40% of pitchers ranked in Baseball America’s top 20 succeed in the majors
•About 30% of position players and 20% of the pitchers ranked 21-100 succeed in the majors
Success and Failure Rates of Top MLB Prospects - Royals Review