Fleeing from the war that has raged on the planet Cybertron for millions of years, the heroic Autobots led by Optimus Prime encounter a surprise attack by the evil Decepticons led by Megatron. The ensuing melee aboard the Autobot ship ends when the ship crashes on a volcano. Four million years later, an earthquake reactivates the ship`s computer and resurrects both the Autobots and Decepticons, resuming the great war of the Transformers. 
(Source: AniDB)

Headmasters starts with Galvatron leading a new batch of Destrons to wage war on Seibertron, the Destron Headmasters. The Cybertrons are rescued by the arrival of the Cybertron Headmasters, led by Fortress (Cerebros, the head of Fortress Maximus). It is revealed that Fortress left Seibertron millions of years ago in search of energy, and have finally managed to come home. He explains that the Headmasters are from a planet called Master; the human-sized robots who live there built themselves Transformers-sized bodies. They can then transform themselves into the heads of the robots, and have now joined the Cybertron-Destron war.
 
(Source: Anime News Network)

It is the year 2005. Twenty-one years after the heroic Autobots and the evil Decepticons resumed their neverending war on planet Earth, the Decepticons have conquered the robots' home planet Cybertron. After a surprise attack by the Decepticons, both factions wage a gruesome battle at Autobot City. In the midst of the battle, Autobot leader Optimus Prime dies during his fight with Decepticon leader Megatron. The Autobot Matrix of Leadership is then passed on to second-in-command Ultra Magnus. Meanwhile, a badly-damaged Megatron is jettisoned by Starscream into deep space, where he encounters the planet-eating robot Unicron and is reborn as Galvatron, the new Decepticon leader. With Galvatron's reign on the rise and Unicron's imminent arrival within Cybertron's orbit, the Autobots must act quickly and protect the Matrix or face total annihilation. 
(Source: Anime News Network)

Fight! Super Robot Lifeform Transformers: The Comics collects every issue of the original Generation 1 Transformers manga published in the pages of TV Magazine. Fight! Super Robot Lifeform Transformers Prologue (2 issues, 05/85-06/85) 
Hundreds of thousands of years ago there existed a highly-advanced planet called Cybertron. The planet was controlled by two factions of super robot lifeforms: the heroic Autobots and the evil Decepticons. 
Their endless war drained Cybertron of all its energy, leading to both factions leaving the planet in search of new energy sources. Their battle raged on, eventually reaching the vicinity of prehistoric Earth. Fight! Super Robot Lifeform Transformers (8 issues, 04/86-11/86) 
Trouble is brewing in Tokyo, Japan &ndash; Starscream, Skywarp and Thundercracker are on the attack, out to pillage energy and cause some general destruction. But the Autobots have pursued their foes to Japan, and Optimus Prime, Smokescreen, Wheeljack, Trailbreaker and Sideswipe speed onto the scene, just in time for Prime to transform and save a young boy named Kenji. The Story of Super Robot Lifeforms: The Transformers (5 issues, 12/86-04/87) 
Responding to an SOS, an Autobot team consisting of Rodimus Prime, Ultra Magnus, Kup, Blurr, Springer and Arcee head into space at full speed, and discover the spaceship that sent the call for help held prisoner by another. The Great Transformer War (3 issues, 04/87-07/87) 
(aka Transformers: Big War) 
The Decepticons have captured Dalton, a brilliant scientist from the planet Elan, but he is refusing to work with them, and the Aerialbots and Protectobots are already on their way towards Trypticon to rescue him. "Great Decisive Battle of Planet Beast!" (special, 08/87) 
With White Leo and Rodimus Prime away, the Decepticons and their Beastformer allies make another attempt to conquer planet Beast. Transformers: The Headmasters (8 issues, 08/87-03/88) 
As the Autobots and the recently-arrived Autobot Headmasters ruminate on the current state of play &ndash; the death of Optimus Prime, their base on the planet Athenia, the power of the Headmasters &ndash; Galvatron leads the Decepticon Headmasters in a plot to destroy Battleship Maximus. Transformers: Super-God Masterforce (12 issues, 04/88-03/89) 
(aka Transformers: Masterforce) 
After the events of The Headmasters, the Autobots and Decepticons have departed Earth... or have they? Transformers: Victory (10 issues, 04/89-01/90) 
The Victory War begins as Star Saber and Deathsaurus face-off on Earth! Transformers: Zone (special, 04/90) 
When nine of the most powerful Decepticons are gathered together under the rule of Violen Jiger, Autobot Powered Master Dai Atlas must step forward to prevent them from acquiring the power of the mystical Zodiac. Transformers: The Battlestars (special, 08/91) 
Super Megatron attempts to pillage energon from an oil rig, only to be confronted by Star Convoy! 
(Information collected from Transformers Wiki and TFArchives).

After being warped from their universe to that of Mazinger, the Transformers join the fight between Mazinger Z and Dr. Hell's army of mechanical beasts. 

A crossover between Mazinger Z and the Transformers series, with each chapter drawn by a different artist.

Starting off as 4koma and published online to promote the titular Transformers Legends toyline, with special Bonus Edition (出張版 Shutchōban) chapters of the comic packed with the toys themselves, it Initially showcased the misadventures of the Beast Wars cast re-imagined as adult Transformers fans, before eventually taking a more story-driven approach and attempting to connect all the entries of the Japanese Generation 1 anime and manga continuity into one storyline. 

Heavily marketed towards adult collectors and otaku in the face of the brand's dwindling popularity with children after TakaraTomy's largely unsuccessful first attempt in the mid-2000s, it attempted to change the image of the Transformers franchise, with much more "adult", often ecchi-filled humour and numerous references to fan culture.
 
Ulltimately concluded when TakaraTomy began a brand unification with Hasbro starting with Power of the Primes, deciding to mainly sell Hasbro toys as is with minimal changes to packaging. It was eventually succeeded by the more action-oriented Generations Selects Special Comic promoting Hasbro and TakaraTomy's joint Generations Selects imprint. (Source: TFwiki, edited)

Beginning with a recap of the coming of the Transformers to Earth and the story of Devastator, the OVA then gets its original story underway, as the Autobots are shown to be in the midst of constructing the powerful "Scramble City," overseen by their newest arrival, Ultra Magnus. 
When the Decepticons learn of this, their combiner robots are deployed to attack, and a battle between them and their Autobot counterparts ensues. 
(Source: Wikipedia)

Near the end of the 20th century, the Transformers form an alliance with the humans. Together they start to develop a large transportation gate named "Trigger" as a symbol of amicability. However, the Decepticons have their eyes on the gate, and so does somebody else. 
(Source: Transformers Wiki)

As 2006 settled in, Earth had been rendered completely devoid of Transformers, and the rebuilding of Tokyo was underway. However, Galvatron's impact was revealed to have had a much greater effect than anyone could have predicted&mdash;the blast caused by his impact had scattered his Unicron-empowered cells throughout the planet's atmosphere. When they came into contact with other animals and objects, from marine life to cars, they fused with them, becoming one of many monstrous creatures referred to as Legion. This catastrophe also created the means to defend the world against the Legion, however&mdash;when Galvatron's cells came into contact with human beings, they also become able to fuse with other entities containing his cells by kissing them. With their Autroopers being the perfect candidates for this "ParasiTech" fusion process, the EDC began recruiting and training these "Kiss Players" as combat squads to battle the Legion. 
(Source: Transformers wiki)

A series of tie-in manga for Takara's Transformers Unite Warriors figurine series, focusing on the Combiners.

A Transformers manga following the adventures of Star Convoy and Galvatron in the Precursor World, from which Primus originates.
 
Note: Each chapter was published online on the TakaraTomy Mall website, in the listings for featured figurines sold as part of the Generations Selects line.

Tie-in manga for Hasbro and Takara's Kre-O blocks Transformers product line. The story follows various comedic shenanigans involving Transformers Kre-O sets and figurines, at times retelling the events of Transformers Generation 1 anime's episodes.
 
Note: Chapter count includes a prologue chapter and a special chapter included in the product catalog.

A manga about the light-hearted misadventures of the Autobots and Decepticons in a setting strongly resembling the original Generation 1 cartoon for a young audience while also promoting various exclusives aimed at older collectors. The web comic additionally inserts character profiles calling out the specific toy being advertised in each issue. 
 
(Source: TFwiki, edited)

Through the machinations of Tarantulas, NAVI-ko is "warped" into a body of her own, which transforms into a dolphin. She debuts her new form to the bemused Megatron as she presents him information (secretly provided by Tarantulas) on "Nemesis Prime", an evil clone of their ancestor, Optimus Prime. Megatron wants to add Nemesis Prime to his own forces, so he sends NAVI-ko back in time via a transwarp portal to Doctor Arkeville's Decepticon Base in Yokohama, Japan, in the year 2014 where Nemesis Prime has been detected. 
 
Note: Tie-in manga released online to promote the 2014 Transformers Expo in Yokohama. 
 
(Source: TFwiki)

Part of a collaboration between the Transformers Franchise and the Super GT sports car racing series. 
 
Set in an alternate continuity where the Cybertrons and Destrons have made peace in favor of organizing an annual friendly competition, the Transformers GT - a race where the Transformers compete, aided by race queen-like entities known as GT Sisters.

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