Transformers

Since the initial conception of the Transformers in the late 1970s and early '80s, various stories have been written or imagined set in a universe where they exist. These universes existed in a very fragmented way - the US cartoon universe is very separate from the US Comics universe, which is in turn expanded on in the UK Comics universe. Then there is the Japanese cartoon, which goes further than the US Cartoon, and then Beast Wars and Beast Machines came along and started adding to all of them.

The Primary universes are:

Generation 1 (or G1)

Note: The term "Generation 1" was originally an inofficial fan term rather than an official term. It was coined as a back-formation from "Generation 2", which really was an official Transformers term right when it was first invented. In the 2000s, however, the term "Generation 1" entered into official use with Hasbro's "commemorative series" rerelease toys and Dreamwave's comic books.

The Transformers (original 1980's series, 4 seasons - later repackaged as "Transformers: Generation 2" animated series)
Transformers The Movie

Beast Wars/Beast Machines

Beast Wars (3 seasons)
Beast Machines (2 seasons)

Some people say that the Beast Wars and Beast Machines cartoon series also take place in the G1 universe, although these series bare little resemblance to the original G1 series.

Japanese Generation 1 (or G1)

Fight! Super Robot Life Transformers! (seasons 1 & 2 of American Transformers series)
Scramble City (Japanese-exclusive OVA to bridge seasons 2 & 3)
Transformers The Movie
Transformers 2010 (season 3 of American Transformers series)
Headmasters (Japanese-exclusive series taking the place of the 4th American season in this continuity)
Super God Masterforce
Transformers: Victory
Transformers: Zone (one-episode OVA, story later completed in manga form)
Beast Wars (Beast Wars season 1)
Beast Wars II (Japanese-exclusive cel-animated series)
Beast Wars Neo (as above)
Bears Wars Metals (Beast Wars seasons 2 & 3)
Beast Wars Returns (Beast Machines)

Marvel Comics Continuity

Generation 1 (80 issues, 4-issue "Headmasters" miniseries, 4-issue G.I. Joe crossover miniseries)
Geneartion 2 (12 issues, preceded by four-issue long crossover in the pages of G.I. Joe)

In the United Kingdom, the American comic series was reprinted in a fortnightly magazine which soon began to run the risk of getting ahead of the US and running out of material to reprint. So to fill in the blanks, original material began to be produced for the UK comic, which began to come into it's own after the inclusion of time-travel and elements taken from the future era introduced in Transformers: The Movie. Some parts of the US comics were re-written for UK audiences, and the G.I. Joe crossover is not part of it's continuity. The UK comic ran to 332 issues before ending. A few years later, there was a short-lived attempt to reprint the G2 comics, which began with two issues of original UK material to replace the G.I. Joe story that preceded it, and then three mores issues of US reprints before it was cancelled.

Dreamwave Continuity

Having obtained the Transformers license in 2002, comics company Dreamwave have created a new Generation One continuity which draws on aspects of various past continuities. It comprises:

"Transformers: Generation One" Vol. 1 (six issues), Vol. 2 (six issues) and Vol. 3 (ongoing)
"Transformers: The War Within" (six issues) and assorted ensuing subtitled six-issue miniseries, telling tales from Cybertron's past
"Micromasters" (four issues)

A profile series, "Transformers: More Than Meets the Eye," has also been release for this universe, and the Dorling Kindersly book, "Transformers: The Ultimate Guide" treats it as the main G1 timeline. Three novels have been released set in this timeline, and a Beast Wars comic was planned that would make the events of the cartoon series part of Dreamwave's universe.

The "Robots in Disguise"/Car Robots Universe

A stand-alone universe with no current ties or reprocussions to any other storyline. In this version, Fire Convoy/Optimus Prime was a fire engine and Gigatron/Megatron a six-changer.

The Modern Cartoon Universe

Includes the Armada, Energon and Cybertron series. In Japan, however, only Micron Densetsu (Armada) and Super Link (Energon) are connected. Galaxy Force (Cybertron) is a separate continuity. Dreamwave Comics (above) have also developed a comic book series for this universe, which is entirely different from the cartoon universe (just as the Marvel G1 comic book differed from the G1 cartoon).

The reasons for the incongruities are manifold; including letting marketing have complete hold over the story (a trend which will continue), and several writers given a blank slate on which to work.

Differences within the universes include, but are definitely not limited to:

The different origins of the planet Cybertron (Formed by Primus (MCG1)) or created by the Quintessons (MTMTE).
The origin of the headmasters (Nebulons in MTMTE, a subset of Transformers in the Japanese series "Headmasters")
Within the G1 MTMTE series, different origins for the Constructicons (Created Megatron, then created BY Megatron)
The sudden appearance of such important plot devices as the Autobot Matrix of Leadership, the Key to Vector Sigma, the Key to the Plasma Energy Chamber, all of which were incorporated into the Dreamwave Comics storyline and books;
The creation of Optimus Prime (Rebuilt from Orion Pax by Alpha Trion (MTMTE), or evolved from Optronix in the Dreamwave Continuum).

Dreamwave, as the most recent holder of the comic/novel license (2003-2005), has taken it upon themselves to adapt Transformers for young adult readers and incorporate a deeper storyline, rewriting the generation one universe in a single, unified style and filling in gaps in Transformers history.