Stephen King... I mean, Sam Miller, at Baseball Prospectus, tells the horror story of the fall of the Astros from their 2004-2005 heights, as seen through the progression of their 29th ranked 2004 farm system. (The full article requires a subscription, but I think the majority of it is available for free). This is a companion piece to his earlier article outlining the Brewers, who were ranked number 1 at the time. If you would like a detailed analysis of what led to the Astros downfall, this is a good read. I can completely understand if you don't though, as it could lead to some vivid nightmares.
I think this a pretty good response to all those people who are devaluing the current strength of the farm system. Sure, a good farm system doesn't guarantee future success. But it sure beats the alternative.