According to the Wikipedia article on Transformers:
However, the Japanese broadcast of the series was supplemented with a newly-produced OVA, Scramble City, before creating entirely new series to continue the storyline, ignoring the 1987 end of the American series. The extended Japanese run consisted of The Headmasters, Super-God Masterforce, Victory and Zone, then in illustrated magazine form as Battlestars: Return of Convoy and Operation: Combination.
After the first season of Beast Wars (comprising 26 episodes) aired in Japan, the Japanese were faced with a problem. The second Canadian season was only 13 episodes long, not enough to warrant airing on Japanese TV. While they waited for the third Canadian season to be completed (thereby making 26 episodes in total when added to season 2), they produced two exclusive cel-animated series of their own, Beast Wars II (also called Beast Wars Second) and Beast Wars Neo, to fill in the gap. Dreamwave retroactively revealed Beast Wars to be the future of their G1 universe, and the 2006 IDW comic book Beast Wars: The Gathering eventually confirmed the Japanese series to be canon within a story set during Season 3.
Robots in Disguise was a purely Japanese creation that was highly censored and then banned from cable TV in the U.S. because its original run in Japan ended at the end of 2001, and it had references to building destruction and terrorism.
In Japan, the series Transformers: Cybertron showed no ties to the previous two series, telling its own story. This caused continuity problems when Hasbro sold Cybertron as a follow-up to Armada/Energon. The writers attempted to change certain plot elements from the Japanese version to remedy this, although this largely added up to nothing more than references to Unicron, Primus, Primes and Minicons.