Gunslinger Girl, Saishuu Heiki Kanojo Recommendations
Both are about stories of girls who were created to be weapons.The stories tell how they deal with their new way of life.
They both tackle the subject of modified girls and are also both extremely serious animes.
Both about girls who are in the wrong place at the wrong time and are turned into weapons of war. They are very similar in tone, and focus on some of the same themes, though SaiKano focuses more on the costs of fighting rather than the costs of being turned into a tool for fighting.
Similar theme in that a young girl/s are being corrupted mentally and physically by an arm of the government. "Is it worth it" as question plays a big role in both anime.