As many of you already know, the Tranformers stories occur in many different Universes making up one Multiverse. Well I'd like to help clear up confusion by compiling a list of all the Universes we know of, as well as what stories are included. If there are any mistakes or anything I missed, please let me know.

The A Universes are ones that the animated cartoons take place in, the C Universes being the comics, and the V, N, and M Universes being Video Games, Novels and Movies respectively.

Universe A1

• The Original Cartoon & Movie
• Headmasters, Masterforce, Victory, and Zone
• G2 (Episodes of G1 Reaired)
• Beast Wars & Beast Machines
• Beast Wars II & Beast Wars Neo
• The Wreckers Convention Comics
• DW's MTMTE Bios
• The Transformers: Universe Convention Comics
• IDW's Beast Wars Comics
• Beast Wars Generations Comics

Universe A2

• Robots in Disguise

Universe A3

• Armada, Energon, & Cybertron

Universe A4

• Transformers: Animated

Universe C1

• Marvel's US and UK Comics
• Marvel's G.I. Joe Comics & G.I. Joe / Transformers Crossovers
• The Headmasters Comics
• Marvel's TF Universe Bios
• The G2 Comics
• IDW's Generations & Other Reprints

Universe C2

• Marvel's Adaptation of the Animated Movie

Universe C3

• Dreamwave's G1 Comics
• The War Within Comics
• DW's Micromaster Comics
• The trilogy of novels, Hardwired, Annihilation, and Fusion

Universe C4

• The Armada / Energon Comics
• The Armada MTMTE Bios

Universe C5

• DW's Transformers / G.I. Joe Comics

Universe C6

• Devil's Due's G.I. Joe vs Transformers Comics

Universe C7

• IDW's Infiltration, Stormbringer, Escalation, & Devastation
• IDW's Spotlight Comics
• Megatron: Origin

Universe C8

• IDW's Evolutions: Hearts of Steel

Universe C9

• IDW's Adaptation of The Animated Movie

Universe C10

• IDW's Prequel and Adaptation of the Live Action Movie
• The Upcoming "Rise of Starscream"

Universe C11

• Transformers: Cybertron: Balancing Act

Universe M1

• The Live Action Movie and it's Upcoming Sequels
• The Novel, Ghosts of Yesterday

Universe V1

• The Japanese Only TF: Tatakai Game for PS2

Universe V2

• The Armada Based PS2 Game

Universe V3

• The Movie Based Game

Universe V4

• Transformers: Autobots for DS

Universe V5

• Transformers: Decepticons for DS

Other Known Universes

• In the Armada Comics, Unicron sends a group of Decepticons from a Universe that we never see, but we can assume it's not one of the existing known universes.
• In the Armada Comics, Optimus Prime gets lost in an alternate Universe that was destroyed by Unicron. It is unknown if this is the same one that Galvatron, Bludgeon, etc were from, but it could be assumed the badly damaged Optimus Prime recovered was from this Universe.
• At the end of the Balancing Act comic, Skyfall is sent to another Universe where we get a glimpse of a "classics" style Megatron.

Notes:

• The Cybertron cartoon does not appear to be in the same Universe as Armada and Energon because the Unicron Singularity had a devastating effect on the fabric of spacetime. This caused all the differences. Also, Cameos by Rad and Kicker in the last episode do imply this is the same Universe.
• The Balancing Act comic features Vector Prime, the very same one shown in the Cybertron Cartoon in Universe A3. Other Autobots from this Universe also make an appearance later in the comic. Also, the Optimus Prime and Ultra Magnus from Universe A2 show up to help after having helped Optimus Primal in Universe A1.

 

Impressive stuff! I don't have nearly enough time to go through all this, but here's a few observations:

Universe A1 - The Japanese series do not comfortably fit into continuity with the US shows, Rebirth is replaced by Headmasters in the Japanese continuity. Really, you need another universe to fit them in:

Universe T1
Generation 1 Seasons 1 + 2
Transformers Car Robots (according to Takara Tomy anyway)
Animated Movie
Kissplayers (sorry)
Season 3 minus the Rebirth
Headmasters
Masterforce
Victory
Zone
Zone manga, Return of Convoy manga, etc.
Japanese G2
Beast Wars Season 1
Beast Wars Second + its movie
Beast Wars Neo
Beast Wars Seasons 2 and 3 (Beast Wars Metals)
Beast Machines (Beast Wars Returns)

I would also place the TF Tatakae game in this continuity, due to the time travel, it could occur at any time)

The IDW comics take an alternate version of Beast Wars Second and Neo, so if you have them in continuity you can't really have the shows. Moreso Second than Neo.
The Dreamwave profile books mainly relate to their comics, BTW. They were written openly, but several of the Dreamwave additions to the mythos like Shockwave's experiments were incorporated.

Universe C2 - you could include the Marvel Movie adaptation into the Marvel continuity, since in the UK comics it did happen in continuity. They flash forward to post-movie events now and then.

I'd also make the novel trilogy their own universe, since they don't sit well with some events of the comics, especially since they follow on from a cartoon episode which by all rights never happened in the Dreamwave continuity.

Cybertron: Balancing Act occurs in continuity with the Cybertron cartoon, Vector Prime uses his time travel abilities to allow him to be in both places at once. It's explained when he suddenly blinks out midway through the story.

Also, the TF Classics comics in the Club Magazine are set in an alternate universe that takes the US Marvel G1 comics as a backstory, but provides an alternate version of the events that follow, in the place of G2.

More realities that have been shown are the Transtech reality from the current club comics, and the universe that Bug Bite comes from (the universe of the Gobots). Also, the UK Movie comic adds two more continuities to the mix - one for their premovie / postmovie events (could possibly fit in with IDW's sequel, depending on how it is written - if Simon Furman is writing Reign of Starscream, take them as one continuity methinks). The other continuity it adds is a grim, alternate reality where Megatron won and now rules Earth, opposed by a small group of Autobots led by Ironhide, Bumblebee and Arcee.

There's also the universe the current Botcon exclusives fit into - a reality where Autobots are evil and Decepticons heroic - the alternate future Deathsaurus comes from (the 2005 boxed set), and the Shokaract reality from the conventions in the late 90s.

All in all, a bloomin' awful lot of realities and I totally commend you for figuring out as much as you have.

 

Great job so far! I need to think about it more, but the only comments I'd add right now...

- Ghosts of Yesterday has some bits and pieces that don't seem to fit in with the continuity of the Movie. Damned if I can remember what they are right now, though. Given the conflicts, it might be necessary to split Ghosts off into it's own universe.
- There was a fourth TF novel that came out after the Hardwired/Annihilation/Fusion trilogy; Legends, I think the title was. It was an anthology with a number of short stories across varying continuities. Some of those stories might fit in with other universes or demand their own realities.
- Universe C1 could sprout off some additional universes as well, depending on where one draws the line between "universe" and "alternate future". That I can think of at the moment, there's the universe from Marvel US G1 where Galvatron/Unicron defeated the Autobots, the post-Movie UK timeline before "Time Wars" and the post-Movie UK timeline after "Time Wars".
- If one wanted to get really nitpicky, the mini-comics that came with the A/E toys might be a different universe as well.

 

Why is the Dreamwave MTMTE series paired with the G1 animated stuff, instead of the Dreamwave comic stuff? (unless the only part of it being counted is the BW prequel bit that brackets the series)

 

Linkage, the comic that came with the Micron Legend DVDs in Japan, belongs in Universe A3 as it is in continuity with Armada.