FFT was the darkest IMO. I don't know how to use spoilers, but there are going to be some so watch out.
Well first off the church created war between two nations which caused massive death to both sides. And it was all so the church could become the major world power. And there was so much betrayal in the game it was hard to keep up. Ramza's own brother killed his father. In a different family (I think it was Vormav's) the father turned into a minion of darkness and kept his kids fighting a war they didn't understand. Your best friend starts to manipulate everyone so one day he can be king. O wait, he is killed by his wife latter on ( Delita and Ovelia married, right). Also, St.Ajora, who was ment to be like the savior to the people turned out to be, well, I don't even know what that thing was you fought at the end of the game, but it was pure evil. The setting itself was pretty "dark". The land just got out of war and now the nobles and church wage another one. And there's the death corps, a group of soldiers fighting to survive. O wait, their leader forsakes his ideals and becomes a minion of darkness. And how Miluda( or was it Wigruf) who gave those speeches on what it ment to be poor was sad. When one of them talks to Ramza about the word meager and eating the same thing every day, I thought that was really sad.