The company's first Visual Novel while simplistic in comparison to the later ones, sums up the first impression of their works very well: DARK. The story follows the life of a young man who sees something he shouldn't have seen, is captured and brainwashed by a shadowy organization called Inferno and then is given the choice "join or die". He is trained as an assassin by a soft-spoken girl called Ein. Ein is Inferno's top assassin, code-named "Phantom" and controlled by the sinister Scythe Master, who also brainwashed the man. The man is given the name Zwei and begins his work at Inferno.
Adult Fear. Picture this scenario: You are a family man that has a daughter, a great marriage, and all is well. Soon after, your neighbor start giving you a new way to "see" things and as a result you immediately Go Mad from the Revelation and killed your wife and daughter. You also lose all sense of reason so when you "see" that neighbor, you rape her (which itself stands out as NF). Yeah, Yousuke had it rough.
Dear God, the rape scene. Seeing the mind-corrupted Yousuke deriving pleasure from Saya's helplessness as he rapes her was too much.
Fuminori in ending 1, where he's locked away in a sanitarium, probably for the rest of his life, and will likely never see Saya again as the two say goodbye forever using text messages on a cell phone passed back and forth underneath his cell door. This ending is achieved if you accept Saya's offer to restore your senses. Ironically enough, this ending has the LEAST amount of death in comparison the other two below yet this one is mainly treated as a Non Standard Game Over.
Dr. Tanbo in ending 2, where Saya "blooms" and every human in the planet changes into her type of life form, but Dr. Tanbo, being high up in the mountains where the spores have trouble reaching, transforms agonizingly slowly over the course of weeks as she completes transcribing Dr. Ougai's research on Saya for her own personal pride. At one point she even chops off one of her arms that had undergone the transformation while the rest of her was still human. This ending is achieved if in the Final Battle Dr. Tanbo didn't appear and Fuminori and Saya kills Kouji.
And finally, Kouji in ending 3, as the only survivor of the Final Battle and last person remaining with knowledge of the now-deceased Saya's true nature and Things Man Was Not Meant to Know has to live knowing he can't talk with anyone about what he's witnessed lest they think he's crazy (which he partially is at this point and likely getting worse), his girlfriend and two best friends dead, and a revolver loaded with one bullet hidden in his bathroom in case the day ever comes he can't take his schizophrenia and hallucinations anymore and commits suicide. In this ending, Dr. Tanbo appears to help Kouji, they both successfully killed Saya, Fuminori kills Dr. Tanbo, and seeing that Saya is dead, Fuminori commits suicide.
This is what you get if Nitro+ creates a Mystery fiction. All the New Gen murders in the game have mysterious elements, particularly the second, in which the dead man has an eight-month old fetus sewn into his stomach; given the age of the fetus, it had to have been removed from the mother's body before birth. It is eventually shown, in flashback, exactly who the mother is and how this happened.
There is also Takumi's red delusions, as the green delusions are lighthearted, funny, and erotic, the red ones are the polar opposite, darker, tragic, and Nightmare Fuel.
Water drip doesn't scary? Now read this link  and  and try to imagine the horror by yourself. For info, one people who are fine with other method is very terrifying about this. Oh and Ayase goes through this thanks to Norose.
Time Travel seems awesome doesn't it? Not if someone else decides to try to hunt you down and that every action caused in that time period results in the Butterfly of Doom.
Another one of the bad endings on Keisuke's route is where he doesn't take the screwdrivers out, leaving Akira to bleed to death. And you want to know how to make the other bad ending worse? Do you? "Akiraaa...I love you."
On one of the Executioner endings, Kiriwar has his way with Akira, then cracks his skull open with Mitsuko while Akira is begging him not to.
One of Shiki's bad endings; after drinking Nano's blood, he goes insane and kills Arbitro and the Executioners. He then tells a bewildered Akira that he has surpassed his weakness and that everything will come under his control. He scares Akira so much that he's practically sobbing. But wait! It gets better! In the ending, where Akira has become a nymphomatic slut who takes pleasure by sleeping around and telling Shiki so he'll kill them, it's heavily implied that he has been driven insane by Shiki's treatment.
After entering Toshima, Akira comes across two guys having sex. One of them Is.Not.Moving.
To add on the above, one of the rules of the Igura is that the winner not only takes the loser's tags but they can do whatever they want to the loser. And, as Keisuke points out, there aren't any females in Toshima...
Sweet Pool only had Urobuchi Gen as an advisor but is still chock full of Squick, Body Horror and Mind Screw. The basic premise has Youji, the main character as the host of the female form of a parasite that makes him give birth to slug-like lumps of meat from his butt. Like Saya no Uta, the endings are Bittersweet at best but Makoto's ending involves him going crazy and eating Youji and due to his insatiable desire starts eating his own arm as well.
Other (other Nitroplus works and collaborations with other companies)