Clear Out, an Autobot who appears in the Wings Universe comic, is designed to resemble the Red Dragon Thunderzord from Mighty Morphin' Power Rangers. (2010)
TVTropes defines the literary trope of the scheming second-in-command as "The Starscream".
RID Landfill (Car Robots Build King) has a unique combination system, where he is formed from four bots, with one forming the arms, allowing for multiple different configurations. (2001)
Animated Safeguard is the TF franchise's only symmetrical combiner, paying direct homage to King of Braves GaoGaiGar. (2008)
Animated Jetfire and Jetstorm's fire/wind theme has its roots in some of the earliest concepts done by artist Sean Galloway, who drew designs for a pair of "fire and wind" robots long before the "final" Derrick Wyatt-designed characters were shown. (2007)
In RID 2001, Side Burn has an obsession with red sports cars...which makes his powered-up form being red very questionable....(2001)
Shattered Glass Drift, the Mech With A Mouth. (2012)
Drift's Deadlock design in Cyberverse was based on a piece of fan art from Guido Guidi, which was itself based on G1 Springer. (Springer being a car/helicopter triple changer, like the live-action Drift) (2020)
Hot Rod is magenta in the 1986 movie because an early prototype for his toy was that colour. the final G1 Hot Rod toy was red, and to this day almost every toy released of him by Hasbro is red. (Takara meanwhile, are usually the ones who properly colour him magenta)
in the Legends manga, a legion of Kickbacks do some unspeakable things. (2017)
Megatron is turned into a Pikachu. (2005)
Grimlock takes flight using his giant new swords. (2021)
Slag was built without emotional dampers to keep his violent nature in check, so once every 4 million years he'd go berserk On one such occasion, the other Dinobots attempted to cover for him while Optimus was inspecting their base. (1990)
several TF toys over the course of the franchise's history have been mistaken for being retools of past figures due to design similarities, when they are in fact new molds that merely share engineering cues.
to prove that a Trypticon toy was feasible at the Titan pricepoint, a Titan Fortress Maximus prototype was disassembled and reassembled into the general shape of a dinosaur. (2016)
Ultra Magnus is rebuilt into the gigantic "Maximus Ambus" (2016)
Blurr's death in the IDW Unicron comic pays homage to the Flash's death in Crisis On Infinite Earths. (2018)
the Decepticon Headmasters attempt to assert their dominance with their "Trio Formation". (1987)
Lugnet gets kicked in the ass. (2008)
the robot mode of the Kingdom Ark toy is designed to resemble The Last Autobot from the Marvel comic. (2021)
the Titan Master of Titans Return Sixshot is designed to resemble Jack, a guy who Sixshot killed in the Headmasters anime. (2016)
the Allspark Almanac 2 officially declared that those weird transforming kids from the G1 commercials were "Reverse Pretenders"
in Beast Machines, the character Savage/Noble is revealed to actually be Megatron in another body. While it's clear that's where his dragon half comes from, it remains unexplained to this day where his wolf half came from. (2000)
in the Transformers/Ghostbusters comic, Megatron rematerializes in a new body based on how he would have appeared in the cancelled Transformers Universe MMORPG. (geddit, cos a ghost turns into a design from a dead video game?) (2019)
Bulkhead's appearance in RID 2015 seems to be physically based on his second Prime Voyager toy. (2017)