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'Initial T', a mysterious shadowy figure who appears in the ending montage seen in Cybertron. (2006)
IDW Nova Prime's design was actually an Optimus Prime design that artist @SketchyFig had made for Hasbro, but was never made as a toy. (2006)
the Prime deluxe Kup toy was very clearly designed to be Ironhide, having been based on a design for Prime Ironhide created by Ken Christiansen, and it was released as Ironhide in Japan.
Why Hasbro released it as Kup instead is unknown. (2012)
Whirl's giant pet scraplet. (2018)
In IDW's Infiltration comic, Bumblebee's holomatter avatar resembles Lindsay Lohan.
E.J. Su confirmed that this was a deliberate reference by him to Herbie: Fully Loaded, a movie about a girl (Lohan) befriending a sentient Volkswagen. (2006)
Airachnid flirts with everyone. (2014)
a common practise in exclusive/non-mainstream Transformers fiction is the use of 'virtual redecoes', in which characters' appearances are based on the designs of existing TF toys, without said toy in those colours existing officially.
the Unicron Of Light was immortalised in plastic twice: first as an extremely rare Lucky Draw Figure in 2004, an as an Encore reissue in 2018:
this cover attempts to pay homage to the iconic Shockwave "The Transformers Are All Dead" cover, but since the comic is 'Optimus Prime' rather than 'The Transformers', in ends up saying "Optimus Prime Are All One". (2018)
various covers over the years have paid homage to this one.