The Agnese Forces sticking pens into their own ears and bursting their eardrums all to just stop the main effect of Index's current spell. The casual ease with which they did it really reinforces the fanatic feel of the forces and makes the danger far more real when not even basic survival instinct can stop them.
When Sister Lucia uses her "carriage wheel shrapnel attack" on Touma. The shrapnel embeds into Touma's arm, then rips itself out!
What happened to Musujime Awaki when she messed up her calculations and found part of her leg stuck in a wall, removing the leg also removed the leg's skin and muscle.
New Testament 3: Cendrillon, using magic based on "Cinderella", can remotely mutilate the feet of anyone who has feet of a different size than hers. Worse, Accelerator explains that if she had used it on him, he wouldn't have been able to block it. The spell ignores distance and obstacles to affect the target instantly, so there are no vectors for him to redirect.
Don't piss off a Reality Warper or he'll suspend you in the air and instantly remove all of the skin from your body. Complete with three close-ups: an arm, the beating heart, and the staring "face". Much worse in the novels, where the character's innards in mentioned scene explode across the room after WITH BLOOD VESSELS AND ORGANS STILL INTACT AND CONNECTED WITH EACH OTHER. Despite this, the person happens to be still alive. And let's not get into any of the sequences that include the clone of said Reality Warper, (thankfully) edited out of the anime adaption.
Exclusive to the light novels: Aureolus Izzard Made a copy of himself that had his memories and thought it was him. It goes crazy when it figures out the truth, and has the power to turn anything it hits with its dart into molten gold, even people.
Accelerator. Pretty much anything he does while in violent mode, including brutally killing 10,000 teenage girls, chewing on at least one of those girls' fingers, executing a team sent after him in the most traumatizing and Mind Rape -y ways possible. And then you factor in his Powers which make him more or less invincible. Unless you are stronger than a nuke or happen to have an ability that trumps his and he can't adapt to (so far, only Touma), he is essentially unkillable.
The scene is more gruesome in the light novel, where he chews on a blob of flesh that he blew off of a fallen Hound Dog's jaw using his looted shotgun, looking far more deranged than any other illustration that he was featured in prior.
New Testament 6: Fraulein Kreutune has grown a monstrous mouth and is driven by instinct to try to eat Last Order's brains. Kakine Teitoku has come back, looking like a white zombie. He's also created an enormous army of copies of himself, as well as demonic rhinoceros beetles. They are all him.
New Testament 7: Swarms of man-eating cockroaches that can also chew through metal, concrete, rubber, and plastic.
New Testament 8: Ollerus and Fiamma of the Right ambush Othinus and attempt to turn her into a fairy to make her weaker, only for the attempt to make her a perfect Magic God, no longer restricted by the 50/50 paradox. She apparently kills them both. She apparently makes Touma's companions disappear and gloats that everything that has happened has gone according to her grand design, then pulls Gungnir out of her eye! Touma desperately charges at her, only for her to declare, "These small fights are such a pain. I think I'll just end the world." Everything, save for Othinus and Kamijou Touma, is apparently annihilated, and the accompanying illustration is a completely black page.
New Testament 9: Imagine yourself in Touma's shoes, trapped in an endless cycle of alternate worlds. Having everyone hate you, even your own parents and teacher, then having someone take your identity, then getting eaten alive, buried alive, paralyzed in a hospital bed and left to rot, and trapped in a pod and launched into space all alone.