Digital Devil Monogatari Megami Tensei

Manga loosely based on Shin Megami Tensei. Plot features totally different characters and story.

Based on the video game "Shin Megami Tensei: if..." for the Super Famicon (later ported to the Sony PlayStation).
"Shin Megami Tensei: if..." is about Karukozaka High School which, along with the students and staff, is magically transported to the realm of Makai: the demon world.

Adaptation of Majin Tensei videogame.
The manga is set after the great war of the late 1990s as Japan begins construction on a new capital city. Earthquakes cause massive destruction and rumors of demons have begun to emerge. The protagonist receives a warning and a demon summoning program.

The terrifying manga based on the hit video game! Nobu is a troubled teenager with a dark past. His old high school was sucked into the Underworld, where he and his fellow students battled hordes of demons led by the Demon Lord, Hazama. However, Nobu and a demon-possessed girl named Yumi managed to claw their way back to the Surface World, hoping to start new lives at new schools. But it isn't long before Nobu uncovers a government conspiracy to raise Hell on Earth, and he and Yumi are once again forced to face their worst nightmares...

(Source: Tokyopop)

While playing a ritual-like children's game called "Persona", students are knocked unconscious. While asleep, they encounter a man named Philemon who bestows several Personas upon them. When they wake up, the youths discover they can summon Personas. 
(Source: Kindan no Aku)

The story centers around a young man who discovers a mysterious card that allows him to summon a Jack Frost. Because of this, he is drawn into a world of demons. 

Based on the trading card game, Dante no Mon.

At the end of the 20th Century, the world is facing destruction from massive earthquakes, bad weather and other abnormal phenomena. In Tokyo, Setsuna Kai, a young boy who lost his mother when he was very small, practices Kendo every day because his goal in life is to become strong. As always, his rival Mirai Kaname defeats him and Setsuna feels sad. On his way home, a messenger from the Devil's World appears before him. This messenger proclaims that the various abnormal changes in the world are the work of the Devil. The world will come to an end unless the Devil is conquered. The only ones who can save the world are the "Devil Children." Thus begins Setsuna's adventure in the Devil's World -ANN

Following the collapse of civilization after a worldwide nuclear war in the year XXXX A.D., demons have begun to emerge. The demon summoning warriors Jin, Jack, and Ayame summon demons to help protect people in their hunt for paradise.
Based on the novel Shin Megami Tensei: Haikyo no Naka no Jin by Yoru Yoshimura.

2003 4koma anthology based on the videogame, "Shin Megami Tensei III: Nocturne."

A comic anthology based on the game Shin Megami Tensei III: Nocturne.

The year is 200X. Jin, Akira and Lena are three child hood friends who like mysterious things. One day in the library, along with the mysterious transfer student Ami, they find the "Akuma Compendium". They chanted an incantation in the book and, to their surprise, devils appeared. Ami then told Jin and Akira that they are the Devil Children that will decide the fate of the world. She hands them their Devil Risers. The group then pass through the "Door of Time" to the land of Valhalla where they fight an evil ruler known as Imperius who plans on conquering all of the world. The Nakama of Jin is Rand, a Sol Lion, and Akira's is Gale, a Hylon.
Source: ANN

Hato no Senki tells the story of a young man named Hato Yokoyama that plays a game called DDS-NET in which players can fight against demons. He encounters a Pixie being attacked by other demons and protects her. When the game prompts him to kill her to receive an item, he refuses and discovers a strange symbol has appeared on his hand. This symbol teleports him to an area where he meets a young girl that Hato assumes to be an NPC. Cu Chulainn appears addressing the girl as princess and assumes Hato is another demon. His demeanor changes when he discovers the icon on Hato's hand and explains that Hato is the Messiah. He asks Hato to become his ally in protecting the princess.

A Persona 3 anthology by various mangaka.

Owari no Kakera is an original story taking place one month prior to the beginning of the original game. It is told mainly from Akihiko Sanada's perspective beginning with him seeing a mysterious humanoid-shaped Shadow while exploring the Tartarus together with Mitsuru Kirijo.

(Source: Megami Tensei Wikia)

An anthology comic of Persona 3 by various mangaka.

A teenager who was orphaned as a young boy returns to the city of his childhood. Shortly after transferring to Gekkoukan High School, he is attacked by Shadows — creatures that feed on the minds of their victims. The assault awakens his Persona, Orpheus, his only chance at defeating these creatures of the night. He soon discovers that he shares this special ability with other students at his new school. From them he learns of the "Dark Hour," a hidden time that exists between one day and the next, swarming with Shadows. He joins the Specialized Extracurricular Execution Squad (SEES), and with his new friends, confronts the threat of the Shadows.
After signing a contract in which he "accepts his fate of his own free will," the main character battles with the other members of SEES against the Greater Shadows, incarnations with traits and appearances similar to those of the first 12 Major Arcana of the Tarot. While this is occurring, he continues to encounter and eventually befriends the child who gave him the contract to sign at the very beginning of the game, an entity who refers to himself as Pharos, and is really the incarnation of Death, the 13th Arcana.

A collection of 4-koma manga of Persona 3 FES.

A collection of stories by various artists.

1. *Carpe Diem* by TSUKIMOTO Telaco.  
The MC - Minato - bought a blue butterfly comb for Aegis during the class trip to Kyoto, which has since been lost somewhere in the school.  Ryoji and Minato end up searching for it.  ~Spoilers regarding Ryoji~

2. *We are Friends* by TAMIYA Komo.  
Upon returning to his room, the MC discovers it has turned into the Velvet Room.  However, the elevator gets stuck and won't move until repairs are made, allowing for Pharos to meet Elizabeth and Igor.

An anthology of Persona 3 FES focusing on the citizens of Tatsumi Port Island.

A Persona 3 FES anthology focusing on the relationship between the female characters and the protagonist.

An anthology of Persona 3 FES by various mangaka.

Following a string of mysterious murders, transfer student Souji Seta and his new friends have followed the legend of the Midnight Channel and found themselves pulled into another dimension! In this twisted TV world, a person’s innermost secrets materialize as a Shadow — an entity that may become a powerful ally, or something much worse...

Based on the popular Persona 4 video game!

(Source: UDON Entertainment)

Following a string of mysterious murders, transfer student Souji Seta and his new friends have followed the legend of the Midnight Channel and found themselves pulled into another dimension! In this twisted TV world, a person’s innermost secrets materialize as a Shadow — an entity that may become a powerful ally, or something much worse...

Based on the popular Persona 4 video game!

(Source: UDON Entertainment)

A set of five official anthologies based on the Persona 4 universe released by Ichijinsha under the DNA Media imprint.

A set of four official anthologies based on the Persona 4 universe and released by Koubunsha.

V.1 - Anthology Comic  
V.2 - Seishun Event Shuffle  
V.3 - Koukiatsu Variety Show  
V.4 - Girls Only!  
V.5 - Boys Only!  
V.6 - Quest Senbon Knock

Year Taisho 20, Kuzunoha Raidou the 14th returned to the Capital as the Protector of the Capital. He stayed in Narumi Detective Agency as a cover for his true job. He was partnered with Gouto-douji, a black cat.
One day, series of strange murders came. The victims were strangely killed, as if they were eaten by a beast. Then, Tae Asakura, their friend, came in and said about a person that is most likely to be a victim. Tae came to the man and wanted to investigate further. Raidou had a bad feeling and came to investigate, but the man was possessed by a demon. He almost killed Raidou, but the body fell down. Only left an empty skin. Raidou knew immediately that the demon was out there. Manticore's the name.
Raidou had no choice but to defeat it. After he defeated it, he found Tae, almost unconcious. Gouto said that the man shouldn't be able to summon a demon because he's not a summoner. 
Someone mysterious is responsible for all this. Although the serial killing stop, the mysterious man is still out there. This mysterious man called out the Marebito Project. He knew that Raidou was the great obstacle for him.
How will things turned out? What is this Marebito Project?

V.1 - Karenna Tenshi  
V.2 - Utsukushiki Akuma

Collection of short stories drawn by different authors.

* c.15: Balloon (by Umetani Chigusa)

The comic anthology follows the female protagonist and not the male protagonist from Persona 3 Portable.

A collection of 4-koma manga of Persona 3 Portable.

V.1 - Persona 3 Portable Comic Anthology  
V.2 - Persona 3 Portable Comic Anthology ~ Dear girls ~

Collection of short stories drawn by different authors.

* c.15: *Go go! Girl* (by Yanagi Yamaro)

An anthology focusing on the male characters of Persona 3 Portable.

An anthology focusing on the female characters of Persona 3 Portable.

The setting of Devil Survivor 2 spans the whole country of Japan. It tells the story of Japanese high-school students who receive emails from a website foretelling their friend's deaths. Mysterious creatures invade the country, and the students enter a pact, enabling them to summon demons from their cell phones with a special Devil Summoning App.

A spin-off manga focusing on Hanamura Yosuke. Published in Persona Magazine issues #02 - #09.

After demons break through into the human world, Tokyo must be quarantined. Without power and stuck in a supernatural warzone, 17-year-old Kazuya has only one hope: he must use the COMP, a device created by his cousin Naoya capable of summoning and subduing demons, to defeat the invaders and take back the city.
(Source: Kodansha USA)

While Japan in desperate situation, 13 "devil survivors" cut deals with devils to obtain abilities to fight against unknown invaders with only 7 days left until a world catastrophe, you need to make crucial decision to survive...

Following the plot of the game, it switches between the viewpoint of different characters as they face off against each other in the tournament. Commonly following the story from the viewpoint of Yu Narukami, Aigis, Yosuke Hanamura, Mitsuru Kirijo, and Naoto Shirogane as they face off against the other characters. Both Yosuke and Aigis face off against Shadow Labrys.

A spin-off set one year after the end of Persona 4, Naoto is asked to investigate the mysterious disappearances of two Yagakoro students by an old detective friend, Touko Aoi. There, she is partnered with Sousei Kurogami, a mechanical detective and a polar opposite to her in terms of personality and methodology. In their first encounter, she awakens to a new persona Amatsu Mikaboshi, which enables her to amplify Sousei's persona ability, Tsukuyomi. Together with Sousei, she discovers the Midnight Site, an anonymous site where judgment is passed on others by five judges named after figures in Japanese mythology—Uzume, Sarutahiko, Omoikane, Tajikarao, and Futotama.
However, it quickly becomes apparent that this case and another under Touko's supervision are related when one of the five judges turns up dead with ballistics pointing to a missing police officer's gun. Naoto and the others must discover the identity of the other judges to protect them and find out the culprit who seeks to kill them.

Based on Persona 4. Each chapter follows a member of the "Investigation Team" as they lead their lives in Inaba

Persona 4 spin off starring Naoto Shirogane

Anthology of shorts based on Shin Megami Tensei IV.

In the year 1492 of the Gregorian Calendar, in the Eastern Kingdom of Mikado...
The Samurai guard the Luxurors and Casualries—the people of Mikado. The wild Samurai Walter seeks to improve his self-taught, but unrefined skill. The Samurai Gina watches keeps a close, worried watch on the wild Walter. One night, the pair, while keeping watch, are suddenly transported to an unknown world...
There, they see a tyrant—a demon that is far stronger than any they have encountered! As a result of the battle with the tyrant, the fate of this pair begins to shift...!

Prayers follows Jonathan and another young boy named Asuma, who both seek to become Samurai. A mysterious samurai saves them when they were young from the fallen angel Amy.

Full name in Japanese: ペルソナ4ジ・アルティマックス ウルトラスープレックスホールドコミックアンソロジー

The story takes place on the last day of the Yasogami High culture festival. During the event, the heroes of Persona 4 see a strange bell tower appear on the school grounds. The heroes of Persona 3 also hear the bell, and are dragged into the future where the Persona 4 cast awaits. The two groups are locked in the school covered in Shadows, but meet two mysterious individuals named Zen and Rei, who have lost their memories. The cast soon learns that Zen and Rei's lost memories may be the key to solving the mystery of the bell tower's sudden appearance.

The manga adaptation of the latest RPG in the Persona series from ATLUS: Persona Q: Shadow of the Labyrinth. One stormy autumn night, the P3 gang is bummed that Gekkoukan High School's Culture Festival was canceled due to the weather. But out of nowhere, they hear a bell begin to ring. The next thing they know...

The manga adaptation of the latest RPG in the Persona series from ATLUS: Persona Q: Shadow of the Labyrinth. The Persona 4 Hero and the Investigation Team are drawn into an alternative Yasogami High School during a culture festival. But out of nowhere, a mysterious bell rang...

The story is a continuation of the events depicted in the game Persona 4 Arena and begins the day after it concludes. The Midnight Channel is back on the air and once again broadcasts a strange advertisement for another fighting tournament christened P-1 Climax, that shows members of the Investigation Team and the Shadow Operatives in combat. Just moments after this, Inaba is subject to a power outage and is engulfed by a bizarre red fog.

(Source: Megami Tensei Wikia)

The comic anthology of the Persona 3 movie.

Collection of short stories surrounding the Persona 5 cast.

Collection of short stories based on Persona 5 made by doujinshi artists. Published by DNA Media Comics (Ichijinsha) .

Stealing hearts and changing society is hard work, and sometimes even the Phantom Thieves need a break. This comic anthology details the everyday adventures of high school heroes beneath the mask!(Source: Yen Press)

The manga is based on Atlus' Shin Megami Tensei: Strange Journey Redux Nintendo 3DS game, and will tell an untold story in the game's world.

(Source: Anime News Network)

Ren Amamiya is about to enter his second year after transferring to Shujin Academy in Tokyo. Following a particular incident, his Persona awakens, and together with his friends they form the “Phantom Thieves of Hearts” to reform hearts of corrupt adults by stealing the source of their distorted desires. Meanwhile, bizarre and inexplicable crimes have been popping up one after another…

The story will feature 28 characters from Persona 3, Persona 4, and Persona 5, including the female protagonist from Persona 3 Portable. They will be trapped in a labyrinthine movie theater with no exit. There they will meet Nagi, a woman with black hair and white clothes, and Hikari, a girl with downcast eyes. [ANN]