I've actually been thinking about a game concept for a while now, which is basically a game that looks like innocent at first, an easy puzzle/visual novel hybrid, but as you continue to play the story suddenly gets very dark as you realize that you're actually playing a mentally deranged person who has been... well, in the name of child friendliness (as much as that's a valid concept here considering the images on page 1), let's say, doing involuntary operations on people. The puzzles you were solving were actually you doing operations, and for the rest of the game, the puzzles would then revolve around you slipping back and forth between the "happy world in your head" and the actual world. Depending on the phase you're in when you solve the puzzle, you'd either get your typical mobile game explosion of effects and a happy "Well done!", or, if you manage to end the puzzle in the actual world - which would be harder - you'd be rewarded with a
Fatality! ending.
As far as actual games go though... I think Path of Exile has a rather sick game world (mainly towards the end of act 3) without trying too hard to be edgy. Nothing beats the homebrew stuff from Japan though...