While these rankings are ultimately subjective -- this is, after all, my opinion of each system's relative merits -- I base them on as broad a collection of information as I can. I've seen many of these prospects, I've talked to many scouts and executives about prospects, and I've talked to team officials about their own systems.
Within each system, I'll rank at least 10 prospects, but these rankings consider everything in each system. Most teams have more than 10 players within their minor leagues who project to be better than replacement-level big leaguers, and all of those guys count. Players who have lost Rookie of the Year eligibility (more than 130 at-bats, 50 innings or 45 days on the active 25-man roster) do not count toward these rankings.
I'd rather have potential stars, even if there's some risk involved, but there's also real value in being able to provide your own fifth starters or utility players without having to pay for them on the open market. That means some teams here toward the top of the list got "credit" for 20 or more players in their systems, whereas those in the bottom third top out around 15 names.
I do favor prospects with higher upsides (or "ceilings") over those with less potential to become stars but higher probability of reaching the majors in some role. Few clubs are able to afford stars on the open market, so developing your own is critical for half or even two-thirds of the franchises in baseball. And if you have a prospect who projects as a star, you have the currency to acquire almost any major leaguer you want. The teams in the top 10 have potential stars and a lot of second-tier prospects with future big league value, while the teams in the bottom 10 don't have much of either, with two clubs lacking any top-100 prospects at all.
I'm most surprised by how unbalanced the farm systems across the game are right now. The top four were easy for me to choose, and the bottom six were too, but there are gulfs between them. To some extent, this is a natural outcome of the process of building a good system, contending, and then graduating or trading off your best prospects to enhance or extend your window of success.
We're also seeing more teams concentrate wholeheartedly on their farm systems, however, to the detriment of the big league club -- it's not "tanking" the way it exists in the NBA, but it is the baseball equivalent. A strong farm system is good only to the extent that it leads to major league wins.