Here is an unofficial continuity system consisting of various reading/viewing orders of all the official Transformers stories only. No Fanfiction. (Missing stories have been substituted with speculative notes.)
There are different types of Transformers continuities. Some continuities have the same stories up to a point.
Generations
This includes the canon: Generation 1, Generation 2, Beast Wars & Beast Machines.
There are 22 continuities:-
Books Continuity - Generations
Complete Works Continuity - Generations
European Continuity - Generations
Cartoon Continuity - Generations
Audio Continuity - Generations
German Comic Continuity - Generations
Grandreams Continuity - Generations
Marvel UK Comic Continuity - Generations
Marvel Amalgamated Comic Continuity - Generations
Marvel UK G2 Comic Continuity - Generations
Marvel US G2 Comic Continuity - Generations
Anime Continuity - Generations
Manga Continuity - Generations
Secrets and Lies Continuity - Generations
Regeneration Continuity - Generations
GI Joe Dreamwave Continuity - Generations
Divided Front Continuity - Generations
Dreamwave Continuity - Generations
Energon Universe Continuity - Generations
GI Joe crossovers Continuity - Generations
Botcon Cartoon Continuity - Generations
Robots in Disguise Continuity - Generations
Unicron Trilogy
This includes the canon: Armada, Energon & Cybertron. There are 4 continuities:-
Books Continuity - Unicron Trilogy
Cartoon Continuity - Unicron Trilogy
Dreamwave Continuity - Unicron Trilogy
Panini Comic Continuity - Unicron Trilogy
Classics
There are 3 continuities:-
Brochures Continuity - Classics
Timelines
There are 5 continuities:-
Transtech Continuity - Timelines
Shattered Glass Continuity - Timelines
Masters and Mayhem Continuity - Timelines
Beast Wars Uprising Continuity - Timelines
Assorted
These are unique continuities. There are 8 continuities:-
Aligned
There are 2 continuities:-
Prime Comic Continuity - Aligned
IDW comics
There are 8 continuities:-
IDW Terminator Comic Continuity
IDW Back to the Future Comic Continuity
IDW Star Trek Comic Continuity
Films
There are 5 continuities:-
Titan Comic Continuity - Films
Video Games Continuity - Films
Legends
There is 1 continuity:-
Angry Birds
There is 1 continuity:-
Rescue Bots
There are 2 continuities:-