This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / Runaways
In the "Escape to New York" arc, the Runaways' ally Dagger is attacked (and possibly sexually assaulted) by someone impersonating her partner Cloak. And it turns out that the culprit was a hospital orderly who had access to her room...
During the Civil War tie-in miniseries, SHIELD declares war on the Runaways (because the agency's been taken over by Maria Hill.) In their opening salvo, SHIELD shoots up Victor, tearing his body apart in a horrific manner. As a follow-up, they send a genocidal alternate-universe Kree soldier who snaps Xavin's neck and then captures Xavin and Karolina, as well as Wiccan and Hulkling of the Young Avengers, and sends all four of them to a black site where they're tortured in front of each other by a fat, ugly, mind-rapey creep.
Said torture is vivisection. Which it's implied he performed on a still-conscious Wiccan and is attempting on Hulkling. Because of Hulkling's healing factor, his organs keep shifting and the cuts on his body keep closing up, meaning that he's repeatedly sliced open. The scene opens with this, as an incredibly unresponsive and dazed-looking Wiccan repeats over and over "I want him to go to sleep, I want him to go to sleep, I want him to go to sleep..." (the doctor realized his magic only works if he can hear the commands, so he plugged Wiccan's ears). Oh, and Xavin's body is left on the floor for no reason other than to psychologically torture Karolina.
In the "Live Fast" arc, Chase temporarily turns against his teammates in an effort to resurrect Gert. The scary thing is how competent he was at being a villain, easily hobbling Nico and Victor and leaving the rest of the team scrambling to catch up.
Also worth mentioning is his kidnapping of Lotus and forcing her to help him find the Gibborim and ask to resurrect Gert. While Lotus wasn't totally innocent, it still was creepy to see him threaten her with Old Lace and seem to seriously contemplate sacrificing her. The cold way he tells her to "set [herself] on fire for all I care" after they part ways is also pretty chilling, considering how he'd never shown anywhere near that level of venom towards anyone before.
Nico's powers seem to grow more and more lethal with each arc. In just the first issue of volume 2, she splits the supervillain Wrecker into several pieces,while keeping him alive. At the end of volume 2,she essentially traps the Yorkes in a timeline where they're doomed to witness their future selves' evil and foolish actions, unable to change anything, until their deaths.
The last arc begins with a party, albeit a kind of depressing one... and then something crashes into the Runaways' house. Right off the bat, Old Lace is dead, and Klara is injured. And then Klara wakes up, scared, bloodied, and confused, and lashes out. The last panels show the beach erupting in a forest of vines. Beware the Nice Ones, indeed...