Sailor Moon CS, at least compared to the anime it's primarily based on.
The superhero parody webcomic Emokid and Chemokid was initially dark comedy, but eventually became a suspenseful story with deep backgrounds and character development while still maintaining the odd sense of humor that only the writer of Head Trip can provide.
In a May 2008 Dominic Deegan strip, the title characters learns, to his horror, that his favorite comic is about to become Darker And Edgier... by retconning the hero into a demon. It's like making Superman Darker And Edgier by giving him a German heritage, a small mustache, and a great personal hatred of Jews.
It was foreshadowed at the end of the Storm of Souls arc. One of the cosmic consequences of breaking the storm was that many of the souls normally bound for Heaven or Hell ended up in the wrong place.
Occurred in A Modest Destiny, around the third story arc. Up to that point it was a lighthearted and humorous fantasy spoof. Then came "The War of Fate" arc, which was much more darker and serious, such as the female lead considering getting an abortion.
Ctrl+Alt+Del. The shift from "two game nerds on a couch" to "personal responsibility and miscarriage tragedy".
Wapsi Square has certainly gotten much darker and edgier since it shifted from a slice-of-life comedy, to a supernatural drama; dragging in themes of suicide, human sacrifice, manifesting personal demons, and a looming quasi-apocalypse.
Breakfast Of The Gods is a Darker and Edgier and Bloodier and Gorier use of breakfast cereal mascots. Tightly-written and exquisitely drawn, it's D&E&B&G at its finest. Frankenberry is a sadistic thug, Sonny the Cuckoo is batshit insane, The Trix Rabbit is a private investigator, Toucan Sam runs a bar and acts a lot like Rick. It's now completed.
Dan and Mab's Furry Adventures started out as a very light-hearted comic that followed the everyday antics of Dan, Mab, and their friends and family. Later on, things like Dan discovering that he is an incubus, Mab being involved in...something that she claims will kill at least two of her friends, a flashback revealing that on Dan's first adventure one of his friends was brutally killed by Dark Pegasus, and all of Abel's Story made it clear that DMFA is definitely a more mature comic than when it started. Though this to be expected, as the comic was started when the author was in high school, and so it's probably matured along with her.
Act 6, being post-Scratch and as such more conducive for the kids to be battle-hardened and able to beat the game, is much darker than its mirror, Act 1. Dirk and Roxy are the only humans left 413 years in the future, Betty Crocker rules the world, the ICP were presidents and Guy Fieri the Antichrist. Post-Scratch Jade got stabbed to death by the Condesce's 2x3dent, PS Dave brutally beheaded the ICP, and PS Rose stabbed Fieri's eyes out with needles and rode his body down a waterfall of blood. Then they died brutally to the Condesce. Hell, at one point, Dirk Portal Cuts his own head off in a Thanatos Gambit to save his friends, two of whom had been impaled through the stomach by an inescapable, planet-obliterating weapon. To reiterate: HE CHOPS HIS OWN HEAD OFF. Kids and fun.
So for a long while, getting killed only meant you got to live out the rest of your existence in a dream bubble with all the other dead people. You could be happy there. Nepeta finally got a version of Karkat to be with, Equius got Aradiabots, a version of God-Tier Tavros was happy and flying free... but then, in [S] Caliborn: Enter, we see that Lord English, hinted to be the final Big Bad of the series, has the ability to destroy the dreambubbles. He is literally killing dead people. Also, his younger self, Caliborn, escapes his prison by gnawing his own goddamn leg off, complete with gratuitously-spurting candy red blood.
Then [S] GAME OVER. occurs, killing off damn well near a good chunk of those who managed to survive any of the above events. Good thing this is a doomed timeline, though...
Sam and Fuzzy parodies the trope here. And then again here. And then manage to further parody the second parody here. Sam Logan does not seem to like this trope.
There was also the student film "Bring Me The Head Of Charlie Brown" by future Simpsons writer Jim Reardon, which involves the Great Pumpkin hiring the kids as hitmen to kill Charlie Brown in gruesome ways, eventually he snaps and goes on a killing spree.