From Baseball America we get their annual Organization Talent Rankings:
We present our annual organization talent rankings, evaluating each farm system based on its prospect-eligible players heading into the 2011 season. Our ratings consider both impact talent and overall depth and were developed by the Baseball America staff.
1. Kansas City Royals
2. Tampa Bay Rays
3. Atlanta Braves
4. Toronto Blue Jays
5. New York Yankees
The Phillies are 10th, Nationals 13th, Mets 20th, and the poor Marlins, who must depend on talent from within to replenish their Major League club, are 29th -- Yikes! Baseball America also ranks each organization...
[...] based on the talent that has passed through it since the end of the 2007 season. That includes both prospects graduated to the big leagues or used in trades, as well as those lost via waivers or the Rule 5 draft.
The Braves come in ninth on this ranking, just below the Marlins (I guess that's one reason the Marlins minor league depth is so low). Nationals are 14th, Phillies 20th, and Mets 26th. The Braves philosophy of a strong farm system that produces talent for the Major League club and to be used in trades can be seen in these two rankings.