The ending with Ted stuck alone in the belly of AM as an immortal blob is pretty horrific, but he is a little happy that the other survivors are no longer being tortured.
The Computer Game
Anytime you can get the characters to smile. It is a small moment that reminds you there is hope even in a situation as terrible as in this game.
Gorrister realizing he was not to blame for Glynnis' insanity, and then giving her one last kiss before burying her.
Benny growing attached to Mutant Child beyond simple necessity, and deciding to give his life to spare him from being sacrificed.
His fellow soldiers forgiving Benny for murdering them in cold blood after planting a beautiful flower on their graves.
Ted overcoming temptation and defeating the devil, allowing Ellen's (or a robot of Ellen) soul to get into heaven. The angel happily tells Ted "God bless you."
In AM's RAM space, Ellen will remark that the Superego looks like an angel, an image of Ted will flash before her, even though she was not in Ted's scenario.
In AM's RAM space, in Gorrister's section, a robot of Glynnis will help weaken the power of the electric generator, and before returning to a pod, will tell Gorrister that her insanity was not all Gorrister's fault, and that they both made mistakes.
Double Subverted with Nimdok's scenario. Yes, he is giving pliers to prisoners so they can escape from the concentration camp, saving a child from having his spinal cord removed, giving a horribly disfigured man ether, defeating his Nazi superiors, and reviving the Golem, but the sheer evil of all his crimes prevents him from receiving redemption, and the best thing he can hope for is a death at the hand of the golem by the old prisoner, who reminds him of his crimes constantly. However, when Nimdok enters his section of AM's RAM space, he finds an arm of the prisoner, with his voice commending him on taking his first step toward accepting what he's done, then asking him to join his fallen brothers.
The good ending, where the final player shuts down the evil supercomputer, revives the last living humans on the moon, begins the process of restoring the Earth to its former glory, and contentedly remarks on being able to watch over the computers in case AM comes back.
This becomes a Tear Jerker at the end when we discover the final purpose of the Hate Pillar: a grave.