According to Sonic Battle, Shadow the Hedgehog is able to reach higher speeds than Sonic thanks to his Air Shoes. Similarly, in IDW #20 Sonic comments that a zombified Shadow is not nearly as fast as usual, due to his inability to use his shoes.
Scratch, Grounder, and Coconuts from Adventures of Sonic the Hedgehog appear in the Archie Comics as the "Super Special Sonic Search and Smash Squad", very minor villains who post-SGW work for Breezie the Hedgehog, who runs an entire media empire.
Pre-SGW, Bunnie was thrown into a Roboticizer and saved halfway through the process. Post-SGW, she was caught in the middle of an Eggman attack and was partially dismembered, with Uncle Chuck using a prototype Medical Roboticizer he built to save her life.
In Archie #195, Eggman builds Metal Sonic with the SXSU-401 engine. This references Metal Sonic's appearances in Sonic X #40 and Sonic Universe #1. Moreover, Snively mentions an STH-25 model, referencing Metal Sonic's comic debut in Sonic the Hedgehog #25.
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.