The Neutral path ending becomes a CMOA for artificial intelligences everywhere, as the "enlightened" Arthur refuses to return to Earth with the crew and detonates the Schwarzwelt from within using a nuclear device strapped to the four Cosmic Eggs, both to save Earth from the Schwarzwelt as well as to prevent mankind from misusing the vast supernatural knowledge he has gained. Arthur, we salute you.
Speaking of the Neutral path: Your teammates cheering you on as you approach Mem Aleph. A Shin Megami Tensei game where you actually get respect for choosing Neutral? Yes, please.
And the crew in the Neutral ending is implied to travel around the world to spread what they learned in the Schwarzwelt, to damn well ensure that another Schwarzwelt doesn't happen. So instead of "kill everything" like series tradition, you get "kill the forces of Law and Chaos, but spare and save humanity."
Mastema as he falls, defeated, in Horologium. He curses you, and rages and screams... and then Louisa Ferre appears, calls him out on his ridiculous pretenses and rubs on his face how low he's fallen.
Watching the demon lords of each sector lose their marbles by means of a Shut Up, Hannibal!.
Talk to the demons in the final sector. If they aren't on your side, they freak out when they realize who you are. You've become so powerful that ancient gods and devils fear you on reputation alone.
Asura's rage-inlicting Asura Roga attack makes the fight against him very frustrating if you try to fight him normally. The solution? Fight him all by yourself, no demon allies, and just heal whenever you're not busy tearing him to shreds.
Occasionally, Horkos summons a minion, which he will eat a few turns later to recover HP. If you inflict a status ailment on the minion, Horkos will contract it upon consumption. Food poisoning!
Having the ultimate That One Attack, M.A, actually fail to hit! Check this out! Go to around 2:56, and watch the impossible happen right before your eyes!
An Offscreen Moment of Awesome for the people of Earth revealed at Carina: when the team contacts the Joint Project for the first time, they learned that the Schwartzwelt has advanced to the point that the Project can no longer cover it up, and demons have been appearing in populated areas. However, it's also stated that in the face of this new threat, all the world's nations have put aside their differences in order to fight back! It gives the player hope that maybe, just maybe, humanity can learn its lesson from the Schwartzwelt crisis after all.