Tough question.
The Folk of the Fringe and Enders Game by Orson Scott Card always stuck with me. Post apocalyptic stories always catch my attention, and it reads so weird and haunting and interestingly. Enders Game is just a great scifi book with good world building.
The Way of Kings is an insane read at over 1,000 pages, but it's a fantasy epic that absolutely crushes any other modern fantasy.
The Secret of NIMH I want to include because it's directed at children, but handles some grim topics and is a really standout way to introduce younger audiences to darker themes in their media. Not over the top dark terrible things, but just content that feels like it treats children like people, giving them important lessons without baby gloves.
Slaughterhouse Five is another one I really like. Dark humor, scathing political commentary, irreverent, it just really goes for it.