Hmm, here are some.
A Cruel God Reigns
Bokura no Hentai
Shamo
Freesia
Teppu
A Cruel God Reigns is a story that opens up on the aftermath of a terrible car accident. Gregory Lowland is on the verge of death in the hospital, while his new wife, Sanda, dies in the accident. When his son, Ian, and his step-son, Jeremy, are at Sandra's funeral, Ian hears him mutter, "He should have died... Why was Sandra in the car?"
I should mention that this manga does deal with a lot of mature issues, such as rape, pedophilia, drug use, and prostitution. Male-on-male sexual assault is a common scene in the first half of the story, which is a flashback to the events leading up to the funeral.
Bokura no Hentai follows the story of 3 young cross-dressing boys, that all do it for a different reason. Marika is a young pre-op transgender girl, that crossdresses to become closer to who she truly is. Yui is a young man that dresses up as his deceased older sister, to get the attention of his mentally unstable mother, who will no longer acknowledge him after her death. Parou is a boy that dresses up for the sake of another boy he's in love with, who raped him when he was younger.
There's not too many chapters of this one done, the scanlation group only does entire volumes, so we see a bulk release maybe once or twice a year.
Shamo is about a man named Ryo Narushima, otherwise known as "Boy A". As a teenager, he brutally murders his parents, who physically abused him and his sister. He gets sent to a youth prison, where he is subsequently broken. The story follows the life of a scared teenager, and the experiences that transform him into the monstrous adult he grows up to be.
This is another one that deals with rape (Both male-on-male, and male-on-female), brutal beatings, and murder.
Freesia takes place in an alternate reality Japan, where prisons have been shut down due to a lack of funds to sustain them. Instead, a new policy known as the Vengeance Act is created, which allows the family of victims to take revenge on the criminal either themselves, or by hiring a proxy to execute them in their place. We follow a former soldier named Hiroshi Kano, who decides to get a job as a proxy. Hiroshi suffers from PTSD, and contends with constant visual and auditory hallucinations. The story takes place from his perspective, as we try to seperate reality, from the delusions inside his head.
Again, this one deals with murder, and sexual assault.
Teppu is about a girl named Natsuo Ishido. She's blessed with superior physical capabilities, and is good at everything she tries. She has grown tired of effortlessly succeeding, and is wishing for something interesting that will force her to work hard. One day she meets a girl named Yuzuko, who is trying to recruit people for a MMA school club. Natsuo refuses to join, but after a fight where she actually loses, she decides that maybe MMA will be worth a try, after all.
It's a great read, where the protagonist is actually petty, anti-social, and highly antagonistic. In any other series, she would be the rival to the main character. It's a tri-monthly publication (That is, it's released FOUR times a year), but it's so good that it's totally worth it to keep up.
Some of my personal favorites, anyway.