Print ads and commercials for Ty the Tasmanian Tiger shown the eponymous Ty dropping in on three hospitalized and highly bandaged characters who bear obvious resemblances to Sonic, Crash Bandicoot, and Spyro the Dragon, all of whom have Ty's signature boomerangs embedded in them somewhere. They all flatline after Ty scares them with a "BOO!".
Print ads for James Pond 2: Codename RoboCod, featured the title fish in what appeared to be an ice cream parlor talking up his new Do-Anything Robot abilities, and Sonic dashing out of frame because he couldn't compete.
In Yu-Gi-Oh! GSTART, Kohaku Yudin's Pixel HERO Deck includes a few Monster Cards that reference this series (among others), including Speed Spike (Sonic), Chaos Needle (Shadow), and Chaos Speed Spike (Super Sonic, complete with an Expy of the Chaos Emeralds). According to the author, Kohaku's design also includes a few cues from Sonic, such as his green eyes, blue leg covering (shared reference to Mega Man), white gloves (shared reference to Mario), and blue spikes in the back of his hair.
At the start of Egg Engines, Emile references a line of Dr. Eggman's from Sonic Generations.
Chugga starts humming the boss music from Sonic the Hedgehog 2 in the final boss fight of LittleBigPlanet, as he says it reminds him of the final boss from that game... which ironically had a different, unique, theme to the regular boss theme that he's humming.
One of the actors in that episode is named Jason Griffith, who shares the same name as the previous voice actor for Sonic. They are often confused for each other, but they have different middle names.
Dino Attack RPG member Kotua in Space was a huge fan of the series, and his writing contains many references to it. Most infamously, Chaos was based upon the water creature of the same name from Sonic Adventure, with the Chaos Emeralds used by Kotua being a recurring element of the series.
The XERRD scientist Dr. Robert Nicholas is inspired by Dr. Ivo "Eggman" Robotnik. Dr. Nicholas was first seen in a hovercraft with a wrecking ball, a tribute to Dr. Robotnik's first boss battle in the first game.
Sonic Romans are introduced inside LuckSore. They are fast and often roll, strike with ring-shaped blades, and a "ring collected" sound is heard when they are defeated. They get some statues and posters in SeizeUs.
Kamiya: In this part, I had just randomly decided to use the word "Eggman". Then I found out it was the name of a character in another famous game. I figured if the fans get a kick out of it, then it is fine to leave it as it is.
The "Change coins into animals" code is not only a reference to the animals in the Prison Egg capsules, but the code (Up, Up, Down, Down, Up, Up, Up, Up) is the same as Sonic The Hedgehog 3's insanely hard level select and sound test code.
In Uniracers, trying to name your team "Sonic" or "Sega" and you'll be told it's "not cool enough." The final boss of the game could also pull a number of Interface Screws on you, one of them being "Hedgehog Speed", which was actually super-slow motion.
The ending of the original Amiga version of Zool has the eponymous character kicking away a tiny blue hedgehog with red shoes. And it has a track of music called "Sonic Basher".
Yoshi's Island included a fast blue hedgehog enemy that was pretty easy to trounce.
In the intro of the obscure Amiga game Quik the Thunder Rabbit, a tiny blue hedgehog is slowly making his way over a road before Quik zooms around the corner, causing the rodent to scurry away and leap off a cliff.
One Simpsons episode has a billboard with "Sonic the Hedgehog says: Wait until marriage" written on it.
In a much earlier episode, Bart is tempted to steal a video game. The Mario Bros., Donkey Kong, and Sonic play the role of bad angels, with Sonic advising Bart to "Just take it! TAKEITTAKEITTAKEITTAKEITTAKEIT!"