The G.U.N. Commander appears in Sonic media post-Shadow the Hedgehog in Sonic Chronicles: The Dark Brotherhood and the Archie comics. In the latter, he is given the name Abraham Tower. Tower and Shadow seem to hold no grudge against each other and delivers missions to Team Dark.
Dr. Starline's shoes have spurs on the heel that are multipurposed, with one setting in particular being for poisoning foes. This parallels real-world platypuses, who have poisonous spurs on the back of their feet.
Shadow Android units appear in Tangle & Whisper #3, their design appears to be based on the two orange Shadows from the Shadow the Hedgehog 2 player mode.
In Archie's adaptation of Sonic Unleashed, it is confirmed that Chaos used their power to keep all of the oceans on Mobius from draining, despite the planet being split into several pieces.
In a flashback within the Archie comics that takes place prior to Sonic Heroes, Neo Metal Sonic and Breezie appear to have mutual feelings for each other.
Amy Rose seems to be the only character in the main Sonic the Hedgehog cast who can handle a casual punch from Knuckles.
Scott Pilgrim's high school band "Sonic & Knuckles" is a very subtle reference to the 1994 Sega Genesis game Sonic & Knuckles.
Sonic the Hedgehog does not know what hedgehogs look like.
Whisper the Wolf's design began with an in-game custom character in Sonic Forces. From there, she would gradually evolve into her final look.
Tails is very discontent with the fact that Eggman has settled on making Tails Doll rather than a Metal Tails. Moreover, this suggests that he finds Metal Sonic and Knuckles to be particularly cool.
When robots or lackeys fail, Eggman uses his built-in command grab
In 2015, it was revealed that Ian Flynn, Tracey Yardley!, and Ben Bates of Archie Sonic the Hedgehog fame had pitched a line of Super Mario comics to Nintendo. It was ultimately rejected. Allegedly, Mario was also intended to cross over with Sonic and Mega Man in comic form.
Knuckles the Echidna's father dies of pancreatic cancer in the Archie Comics.