Adventure Time. Past the post-apocalypticbackstory and severe psychological issues of many of the cast, the show is full of sexual innuendo, thinly veiled references to rape, murder, abuse, suicide, and genocide, and some viciously brutal violence. There are episodes with everything from dealing with a mentally ill loved one to abusive relationships, all wrapped up in the silly adventures of a boy and his dog, with innumerable serious, mature, or just horrifying themes slipped in without technically moving past what is appropriate for children.
Unlike most of Cartoon Network's examples listed, The Amazing World of Gumball actually has a good balance of kids' show humor and adult humornote most likely because the American airings have the show rated TV-Y7, as opposed to the TV-PG ratings that Regular Show, Adventure Time, Clarence, and Steven Universe have, though some will say that ever since season two, the show's Parental Bonus humor and Black Comedy has become slightly more prominentnote though not to the point that the show would be a candidate for [adult swim], like Regular Show has been since day one, such as the dead pizza baby scene in "The Job," the Running Gag of Miss Simian dating Principal Brownnote while shows like The Simpsons and Daria have had teachers dating staff members as seen with Mrs. Krabappel and Principal Skinner and Miss Barch and Mr. O'Neill respectively, The Amazing World of Gumball has Simian and Brown not try to hide it at all, and the ever-growing list of Shout-Outs to music, television shows, video games, films, and real-world situations that either wouldn't interest or be appropriate for the target audience.
Code Lyoko: Tons of tentacle mind rape. Once case of actual tentacle rape from vines. All of the times Aelita died, nearly died, attempted suicide, or had a clone die. All the cursing in Evolution. All of the Fanservice. Aelita seeing her mother kidnapped and her father murdered, on screen. Aelita suffers from flashbacks and hallucinations. Then there was the time Jeremie started acting suicidal and reckless to further his work. X.A.N.A. made so many murder attempts on screen that it can be turned into a drinking game. Franz Hopper went completely insane, as shown through a video diary. And a ton of other horrors.
Courage the Cowardly Dog is packed to the gills with scary scenes, like the screamer girl from "Courage in the Big Stinkin' City", and the blue...something from "Perfect". It ran for four years and got canceled for being too scary, which isn't too surprising. Probably the most controversial episode was "The Mask", where the villain was clearly a pimp who cruelly beat his two charges, with scenes of lesbianism thrown in for good measure.
The Grim Adventures of Billy & Mandy: Not only because the main premise is about two kids that became friends with the Grim Reaper, but also because the show reveled in gross-out humor and the occasional risque joke.
Regular Show. More sex jokes, frequent lethal use of weapons and mild profanities ("crap", "sucks", even "pissed") then you can shake a yardstick at. It's is based on two short films J.G. Quintel made in animation school called "2 in the AM-PM" and "The Naive Man from Lolliland", and while the latter is safe for family viewing (a single use of "hell" wouldn't phase most viewers), the former isn't — at least, by Cartoon Network's already selective standards.
Robotomy: Excessive violence, a lot of Comedic Sociopathy, some sexual innuendo, some mild swearing (mostly words like "crap," "sucks" or "screwed"). One of the show creators worked on Superjail! and it has the look and feel of a Superjail spin-off or companion show.
Scooby-Doo! Mystery Incorporated, which is pretty much Scooby Doo if it wasn't so campy and 1960s. Despite being rated TV-Y7-FV, the show includes moments of death, extreme violence, Black Comedy and the season one Big Bad being revealed to have kidnapped Fred from his birth parents and threatening to harm him if they ever came back for him; to make things crazier, the Bigger Bad is an Eldritch Abomination that the gang had to kill in order to save the Universe. Not to mention an abnormally high amount of Stuff Blowing Up very realistically, up to the point where near the end of the series, roughly half of Crystal Cove is gone! Its Shout Outs skewed heavily toward the adult side of the audience as well, referencing everything from Twin Peaks to Hellraiser to Stanley Kubrick's The Shining.
Time Squad: Here's an apt description of the show: on the outside, it was a funny, unassuming edutainment cartoon (that was more entertainment than education) about an orphaned history whiz taken in by a Time Cop and his Robot Buddy to the future where, each episode, they go back in time to fix history. On the inside, it had more Ho Yay than the original Star Trek, got away with more adult jokes than Rocko's Modern Life, played up the Hilariously Abusive Childhood trope for laughs more than The Simpsons and South Park combined, and seemed to indulge in more homoerotic subtext than anything Oscar Wilde has written. Is it any wonder that Cartoon Network aired it at five in the morning during its final years?
The subplot in "Beneath" heavily implies that the mother of one of Jaime Reyes' friends is being physically abused by her boyfriend. The same episode also reveals that Queen Bee is essentially running a child-trafficking ring, where innocent teenagers are kidnapped and sold to aliens who use them for experimentation.
One of the protagonists' favorite tactic is Mind Rape. And it is played out for maximum shock value.
Gravity Falls wouldn't be too out of place in modern day Cartoon Network, what with the scary imagery and blatant adult jokes that would pass over a kid's heads.
Avatar: The Last Airbender is a show about a war that has lasted for a hundred years, tearing apart families and nations and was begun with the genocide of an entire people. The protagonist, the 12-year-old last survivor of said people, assembles a team of Child Soldiers and trains to overthrow the Evil Overlord (who happens to be a shockingly abusive parent) that seeks to subjugate or kill anyone who isn't Fire Nation.
The "Southern Raiders" episode in general, for its portrayal of murder, revenge and forgiveness. It doesn't go the way one might expect.
The Legend of Korra is a weird example because its content limitations are its biggest concession to its kid audience... and that's not saying much, given how disturbing its violence can get. Its characters have, at various points, committed Murder-Suicide, had a spirit ripped out of their eyes and throat, been graphically suffocated on-screen, accidentally blown off their own head, suffered mercury poisoning, and been electrocuted to death, but that's not what makes it seem like the kid audience was an afterthought. Instead, the themes are what really makes it feel like adults and teenagers were the real target — not only does it tackle such controversial topics as child abuse, social inequality, terrorism and the less-than-helpful totalitarian governmental responses it can spark, anarchy and the dangers of revolution, and depression, it also gives a ton of focus to the fifty-year-olds in its cast and their mid-life family issues. There isn't even a real kid perspective, because Korra's much more young adult than teenager (even if she's only seventeen).
Invader Zim was more grotesque than most of Nick's other works, featured things like children summoning demons and a disturbing amount of body horror (including one kid getting his eyes plucked out), and was created by a man who wrote a comic series about a homicidal maniac. It's kind of in between this and its sister trope, very clearly meant for a young teen audience, but for whatever reason Nick shoehorned it in a block that was otherwise targeted at a different demographic that the show was completely inappropriate for. That said, it's still questionable for even the intended demographic - while it's toned down from JCV's comics, it's basically a hair away from Squee in terms of content, which is very solidly meant for adults.
Rocko's Modern Life, while tame compared to Ren & Stimpy, still has its moments. Social satire runs rampant throughout the series, some of the adult humor is flat out extreme and ridiculous, a few of its worst innuendos got banned from even the DVDs, one of the episodes was banned for being too sexually sleazy, a lot of crazy and disturbing stuff happens in general, there is often serious abuse going on between characters, and the theme song shows what a sick mockery Rocko's childhood was.
Teenage Mutant Ninja Turtles (2012) had driven towards a darker territory in season 2 with frequent disturbing mutations, sexual jokes, some drug references, and in the season 2 finale, the turtles and friends being forced to flee their doomed city homes.
Freds Head goes one step further than the above shows with things like swearing, handling of mature situations outright, and other non-kid friendly material. Unsurprisingly, the show wasn't renewed for a second season.