Sure, it's nice to have baseball's best farm system -- but the truth is that it's still one degree removed from the thing you actually want. Baseball franchises want to win games -- and if you aren't a winning team, at least a good farm system is a nice consolation.
Some teams near the bottom of these farm system rankings are there because they're either winning all the time (often subtracting prospects as often as they're adding them) or have recently graduated a bunch of good young core players and are waiting on the next wave(s). Those are both great outcomes and how this is supposed to work.
As you peruse (other than checking in on your favorite team), focus on the teams that don't fit this rubric: losing teams near the bottom of the farm rankings or contenders near the top. These are the two groups where general managers get fired (the former) and the clubs from which their replacements will be chosen (the latter). The Los Angeles Dodgers and Tampa Bay Rays are seen as the gold star examples -- perennial contenders with top-tier farm systems that every team is trying to copy.
The dollar amounts for each farm system come from projecting what each is expected to do using historical examples. With that, it's pretty easy to project how much they'll be paid in their six-plus cost-controlled years for that projected performance, adjust for time value of money/performance, apply the price teams pay per win on the free agent market for how much that performance is worth, and poof: each player has a dollar value. Then, you simply add up the values for each prospect and have the surplus value of the whole farm system. The latest version of these calculations was done at FanGraphs by Craig Edwards.