In the Archie comics, the song "E.G.G.M.A.N.", from Sonic Adventure 2 appears to exist in-universe, as Eggman sings it to himself in Sonic Universe #39. Whether or not the song exists in it's entirety is unknown.

Deltarune's Susie refers to the act of turning Noelle into a robot as being "roboticized", a term that was popularized by the Saturday morning Sonic the Hedgehog cartoon and Archie's Sonic comics.

Shadow the Hedgehog has achieved the unique feat of warping between three different comics back to back. In-universe, he warps from Moebius to the world of Sonic X, over to the Sol Dimension, then back to Mobius. This goes from StH, to Sonic X, finally ending in Sonic Universe.

Multiple Archie Sonic comics feature plug & play technology where the reader can grab their Sega Genesis controller and guide Sonic through a segment of the story. One of these instances is a scripted quick time event where Sonic loses at the fault of the reader/player.

The Society for Observing and Neutralizing Interdimensional Creatures and Xenomorphs is an organization founded by several individuals who's lives Sonic had ruined through largely indirect means. When told of S.O.N.I.C.X.'s name, Sonic the Hedgehog takes great amusement in it.