It wasn't always like this. Entering both the 2009 and 2010 seasons, Baseball America rated Houston's system as the worst in the game, which proved to be a harbinger of doom at the Major League level. But since then, the Astros have drafted much better and engineered several trades, pumping some much-needed young talent into the organization.
Now, Jonathan Mayo says Nay, it's the Pirates who have the best farm system in baseball.
Houston is a worthy choice, but I've gone in another direction. When trying to decide which organization has the best farm system, I try to look for a combination of impact talent -- elite prospects who could become highly productive big leaguers -- as well as depth. Taking those variables into account, I have to go with the Pittsburgh Pirates.