Bendis once commented that his daughter, who was not aware of the original Spider-Man's backstory and just started to read dad's comics, was shocked when Uncle Ben died.
In issue 13 of the relaunch, both the original Peter and Jameson are tied up after being caught by the Chameleon siblings. While the brother was robbing a bank as Spider-Man, the sister took on the face of J. Jonah Jameson (but with a scantily clad female body) proceeded to shoot the original Jameson in the head. Right in front of Peter. Ugh.
The story line (a follow-up to Longshot's debut in Ultimate X-Men) in which Deadpool, who in this continuity is an Ax-Crazy mutant-hating bigot who traded in any lighthearted humor he had for racist gallows humor and kills for pleasure instead of money, and the mercenaries take Spider-Man and the X-Men to face "justice" on that game show. It starts with a school full of unsuspecting people getting knocked out and kidnapped and ends with them having to rescue Xavier, who is stripped, chained up, and has his eyes pried open Ala A Clockwork Orange, so he is forced to watch his students be killed while being unable to help in any way. Not to mention Deadpool's face is actually a casing that shows a skinless face and exposed brain and despite being defeated it's shown he is still at large in the end.
Venom's portrayal in this series is absolutely nightmarish. The suit, rather than simply making you more aggressive like in the mainstream verse, seemingly drives its wearer to near insanity even giving them delusions to make them attack people (Peter ditches it after it makes him see a random burglar as Uncle Ben's killer before driving him into a murderous rage). Also it apparently feeds off its hosts like a parasite, driving them to try and consume people to stabilize itself in the most graphic detail. And it gets even worse after getting attached to Conrad Marcus; he becomes a hulking Implacable Man monster that Miles can barely hurt and unlike Eddie Brock, he goes hunting after Miles' family and friends, ending with him tearing through a hospital trying to kill Miles' nurse mother, Rio. And he succeeds.
Gwen Stacy's death at the hands of Carnage was absolutely bloodcurdling as she slowly has the life drained from her before being left an empty husk.
Norman Osborn's insanity proves to be exceptionally terrifying in its effect on Peter's life and social circle. The man is so deranged he had his son Harry brainwashed and mentally triggered to better control him and ends up brutally killing him for getting in his way. However, he's so delusional that he pins all the blame on Spider Man to the point he declares God wants him to kill Peter and his friends before going to do just that. Even the other members of the Sinister Six are terrified of him and follow his orders out of fear he would kill them or destroy their lives if not out of mutual benefit.
Nick Fury is this towards Peter Parker especially in how he tries to manipulate fifteen year old Peter's life for his own ends and the fact he brought an entire Spider Slayer regiment to his home and fired on his family to the point the Fantastic Four had to intervene to stop it all for simply slugging him as punishment for Fury endangering his friends. Keep in mind, Fury is supposed to be the good guy in most situations.
Eddie hunts Trask down to his "golf course prison" ready to get revenge. When Trask stammers about the guards, Eddie becomes Venom and says in a terrifying tone "They are not nearly well armed enough." His victim doesn't last long. Then again, as stated above on this page, Venom in general qualifies.
The bomber mooks in the GBA version. They sound nearly demonic when you hit them, and one of their versions can be shown laughing maniacally before they see you coming. This one even shoots fire from both sides when he gets back up. Jeez.