The SNES Fire Emblem's feature, by far, the most mature and dark content of the series. Genealogy/Thracia 776 feature child hunting and village slaughters, as well as some incest thrown into the mix. One of the more disturbing pieces of story I found from these games was in Thracia 776:
Let me know what you think, and I'd love to hear from others what they found within the Fire Emblem games to be disturbing or surprisingly dark.