A few other systems deserve some kudos, so I'll rank the top half-dozen below:
My full story is here.
Jonathan's choice, which he explains here, was a close second for me. St. Louis has impressive depth (Matt Adams, Matt Carpenter, Allen Craig, David Freese, Jaime Garcia, Jon Jay, Lance Lynn, Carlos Martinez, Shelby Miller, Trevor Rosenthal, Michael Wacha, Kolten Wong), but Washington's star power dazzled me more.
Atlanta came up with five building blocks (Freddie Freeman, Jason Heyward, Craig Kimbrel, Andrelton Simmons, Julio Teheran) and several useful players (Evan Gattis, Mike Minor and Alex Wood, among others).
Kansas City nearly rode its system to a World Series championship last year, building the second-most homegrown playoff team in 2014 -- behind only St. Louis. The Royals' in-house highlights included Kelvin Herrera, Greg Holland, Eric Hosmer, Mike Moustakas, Wil Myers and Jake Odorizzi (the key pieces in the James Shields trade), Salvador Perez and Yordano Ventura.
Cincinnati has harvested a nice combination of blue-chip talent (Aroldis Chapman, Todd Frazier, Billy Hamilton, Devin Mesoraco) and solid contributors (most notably, Yonder Alonso, Brad Boxberger, Zack Cozart, Didi Gregorius, Yasmani Grandal and Mike Leake), though it has traded most of the latter group.
While the best is yet to come from MLBPipeline.com's top-rated system, it has produced Arismendy Alcantara, Chris Archer, Javier Baez, Starlin Castro and Anthony Rizzo in recent years.