Teenage Mutant Ninja Turtles the 2003 series. The first five seasons of this series (which span 116 episodes) were not just great in many ways, but also very dark. Although lighthearted enough for children to enjoy, this show deals with personal hardships, torture, death, murder, and misery. The character of Baxter Stockman is always being tortured and mutilated as an act of punishment for his failures, while still being forced to work for the Shredder, who he despises very much. If that's not dark, then I don't know what is. There are also some pretty intense action scenes which depict the turtles being killed, injured, or impaled. Another thing I really like about this series is how Leonardo's character goes through a deep development after the events of season 3's finale. He becomes a much more darker character due to the punishment his brothers went through when fighting with the Shredder, which he feels responsible for. He begins to show an angrier side while also thirsting for success to the point where he lashes out at his father and is forced to work under a new master. I seriously recommend anyone watch this show if they want to enjoy deep plots, great action, fun characters, and a serious tone.
Below are a list of episodes which I feel are some of Teenage Mutant Ninja Turtles' darkest moments.
Same as it Never Was
I, Monster
Bad Day
Scion of the Shredder
Insane in the Membrane
Adventures in Turtle Sitting
Yes, Batman The Animated Series is a must. Can't get anymore classic than that.