- The names of Sonic and Sally's future offspring are Sonia and Manik, the names of Sonic's siblings in Sonic Underground.
- On the title page for one issue, Nack's description is listed as "Fanged Sniper", a reference to his Japanese name, Fang the Sniper.
- Sonic remarks that he beat Scratch, Grounder, and Coconuts when he was eight, which is the age he would have been when you subtract the number of years ago Adventures of Sonic the Hedgehog aired from his current age. And also approximately the time since they appeared in the second issue.
- When Eggman escapes from the Eggdome in #205 in a giant tortoise robot, he shouts, "I will destroy the blue one, you know! He's the obstacle that always gets in my way!" Also see Ascended Meme.
- Ian Flynn seems to enjoy having these in combination with Ascended Meme, such as Metal Sonic saying "It's no use!" at one point to Silver. Silver then responds with "Hey, Metal Sonic! You're too slow!"
- Arlo (one of the Substitute Freedom Fighters) is an armadillo, but has a totally different design than Mighty. It's explained in the Encyclopedia that Arlo is a Western armadillo, while Mighty is an Eastern one. This is a likely a reference that Arlo was created by the American comic team, while Mighty was designed by the Japanese game designers.
- Post-reboot, Sonic and Tails meet up with Uncle Chuck and Muttski in Wood Zone, which was one of the cut stages from Sonic the Hedgehog 2.
- The Freedom Fighter's flying ship's name (The Sky Patrol) is a reference to the spinoff game Tails' Skypatrol.
- #269 features advertisements for HEXAeco and MeteorTech, the latter of which is apparently under new, "non-evil" management. Not to mention Sonic fighting Segata Sanshiro. #270 likewise has ads for Chao Boom, Sonic Man, and Chao in Space 3.
- There's a subtle one in the introduction of the handheld supercomputer Nicole: In the cartoon, Sonic develops a bit of a habit of shaking her when the words she uses get too big for him. It's funny, but more than a little uncomfortable. In the comic, it's the first thing Sonic tries with her until she fights back by shocking him.Sally: That wasn't very nice, Nicole!
Nicole: Neither was nearly shaking me to pieces! - Issue #272 has a guest appearance by Professor von Schlemmer, who is a scientist from Silver's time in the future. The Sonic Championship arc has Wes Weasely as the fight announcer.
- Anti-Sonic's redesign from "Sonic in shades and a leather jacket" into the green-colored Scourge the Hedgehog is a two-fer. Firstly, it homages the famous "Ashura the Hedgehog" glitch-character from the videogames. Secondly, Fleetway's Sonic the Comic had its own green-furred evil Sonic doppelganger, all the way back in 1994! The story "The Pretender" in issue #31 has "Cosmic the Hedgehog", who looks like a green Sonic wearing a cape and a yellow C on his chest, as well as sporting a single blonde curl of hair on his forehead that looks like a C; Cosmic turns out to be a disguise for shapeshifting villainess Metamorphia.
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