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!.
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.