So I recently watched Madoka and I liked it a lot, now I'm looking for something "similar". Let me be a bit more specific, I want something similar more in an aesthetic and thematic sense than in simply being a 2edgy4u deconstruction. Stuff that looks cutesy and girly but is actually fucked up beneath the surface. I've also watched Yuki Yuna and liked it once the truth was revealed. So stuff among those lines. Can be an anime or games, graphics novels, etc....
Martian Successor Nadesico fits your bill so hard that it superscedes it.
Basically any comedy manga by Go Nagai (Harenchi Gakuen, Mazinger Z, Cutie Honey) They look cutesy but Nagai has a pretty edgy sense of humor so there's usually a shit ton of gore and nudity.
Devil Survivor is okay.
Revolutionary Girl Utena.
Berserk (specifically the anime) looks like a pretty typical medieval manga, but the world gets progressively more "dark fantasy" with heavy themes of existentialism.
Which spoiler are you talking about? Anyhow yes, the characters are great, the narrative unfolds in a very enticing way plus the visual direction and art are just magnificent. Check out the movie after as well.
Selector Infected WiXoss and Selector Spread WiXoss, was a really good anime, I really like the contrast between them like Madoka. They never knew anything about each other up until this Hunger Games tier type of a plot rolled in and changed their lives forever.
Nurse Angel Ririka is an early "dark" magical girl anime. It's 35 episodes long, so it takes a while before the evil guys start winning. Also, the last half of the anime is like 240p if you want subs, but that's its charm point.