Hey, this time I'm looking for a series that has a darker side to it. Maybe events that are totally unexpected. Like, a certain manga may look like like your average Shoujo with the cute girl and unrequited love, but once you start reading it, murder, horror, dark humor/themes, or a mind blowing plot arises. Another option is that the Author isn't afraid of inflicting pain or injury on the female protagonist. For comedy reasons or not. I've taken a fond interest in being surprised 🙂 Unfortunetly, the only ones I take note of are anime. I'd like to see some manga too. 

Some examples are:
Jinrui Wa Suitai Shimashita - It looks cute and perfect for the whole family, until you are hit in the face with a mind boggling plot and dark humor. But with good kind of hit. 

Mahou Shoujo Madoka Magica - This also looks cute. Characters are all lovely, and the plot seems cute, fluffy and heroic. Until the series grabs your head and starts dragging you through some deep, intense and dark brown shit. But you end up loving that shit. 

Rec - Kimi ga Naita Hi - Looks like your average Shoujo. Cute 'n fluffy stuff. Outcast girl and popular boy. Nothing new. Until you understand reasons behind certain stuff. Love it.

Sekai no Hate - Hohohoho, Shoujo goodness. Not really. The summary really means what it says. 

Ouji to Hero - There are so many clichés in here, its not even funny. But it's cute and an enjoyable read. I don't know if I'm over thinking this, but even though this manga is cloaked in its protective cliché, there is a darker theme to this manga. A dark undertone. The reason I think this is because the males jealousy seems depicted in a mature, violent way. It's in their eyes. O.O

Please exclude the following:
-Yuri/Yaoi
-Eichii
-Hentai (A little smut or sex on the side is okay)
-Marysue
-Harems (Unless they all don't actually like him/her and are acting that way because of some dark reason)

Suashi no Meteorite - looks like fun and games until:

you find out what happened to the other gods and their followers

I actually had to look up "Mood Whiplash" on tvtropes for this, but this is what I've found (that I've read)...

Higurashi no Naku Koro ni Not a perfect fit, but a very nice and peaceful slice-of-life suddenly turning into a gory horror action is definitely deserving of a mention.

Kamisama Dolls Everything seems all fun and games until Aki appears. Then, everything all kind of goes downhill from there. There's also a dark/tragic past in here. Yup.

Saikano The first chapter seemed just like a regular shoujo romance. Then, things happen, and everything becomes really dark and tragic really quickly.

Zettai Karen Children When I first started reading, I had expected it to be some boring shounen, moe comedy. It was that way for a while, then it got better, and kept on getting better, until it dealt with some really interesting issues regarding discrimination and privilege. There's also a surprisingly dark future awaiting our protagonists... (Also, this might be labeled harem, but it isn't. Not really. Trust me.)

(Oh, and if you don't mind an anime recommendation, I wholeheartedly recommend Princess Tutu. I have no words to describe how amazing and tragic it is.)

Koharu no Hibi? (Not so sure this fits)

First one I had to think of, after reading this topic, was definitely Korosareru nara, Isso Sakura no Ki no Shita de and a few other Mangas by SAKURADA Hina. ^^" Aside from them, the following ones may suit your taste ...

• H - Well, the storyline may start of as usual with a high school student transferring, getting dumped by her boyfriend and meeting her new teacher, but this is just the beginning of quite dramatic and unconventional developments.

• Mayonaka no Ariadone and Coelacanth - Both have got an atmosphere that is full of tension and can't be compared to most of the Shoujo Manga out there, even if they include some well-known elements.

• The Bride of the Water God - If you don't mind Manhwa and a storyline, that includes many twists and characters, then you can find some unexpected sadistic and pretty dark sides to the characters of this one.

"It's like love is a bonus in your life. Even without it, I'm just fine. I don't feel like pointlessly searching for it. You don't have to make yourself unhappy." (Ookami Shoujo to Kuro Ouji)

"Why does it rain?" - "To create drama." (Drops (Andou Yuki))

Hunter x Hunter

Don't be fooled by the cutesy, adventurous first few chapters. It's a cruel world and the protagonist is going to find that out soon enough.

If you like webtoon:
Melo Holic I was tricked by the early chapter and truly believe that this will be the ultimate classic romance. But then the story kicks in.
Nowhere Boy