Baseball America's annual farm system rankings are out, with a few changes from their 2011 Handbook due to the Matt Garza trade. The Rays' haul pushed them to #2 over the Braves, while the Cubs' losses knocked them from #8 to #16.
For more farm system rankings, check out ESPN's Keith Law and Baseball Prospectus' Kevin Goldstein. Keep in mind that graduating prospects to the bigs is a bad thing for a team in these rankings, which as Law notes represent a snapshot. Also, Goldstein provides haikus.
If you look at rankings from all three side-by-side, you'll see that there is a consensus that the Royals, Rays, and Braves should be ranked #1, 2, and 3. The Blue Jays, Yankees, and Reds have consensus top ten systems, with Toronto placing no worse than fifth. There is also agreement that the Astros, Marlins, and Brewers belong in the bottom five. Outliers: BA dislikes the A's and Angels more than the others, Law isn't as high on the Indians but likes the Cardinals and D'Backs, and BA likes the Dodgers more than the others.