- During the Knuckles solo comic run, Echidnapolis was routinely swarming with landspeeders.
- Early stories featuring Robo Robotnik (later to return as Dr. Eggman) and a "good" Robotnik (a kindly veterinarian in that universe, constantly being combated by evil Sonic and friends) were a pastiche on the DC Multiverse. The messenger from the alternate universe is a half-cyborg hedgehog in a biker jacket.
- One particular example is M, Robotnik's android "daughter." She's a sunglasses wearing android Made of Iron, who eventually gets her outer shell blown off to reveal a skeletal-looking body underneath. Now what does this remind you of? To add to it, there's the fact that she looks like a female version of Arnold.
- A supplemental piece of art for an earlier comic was also a homage to Disney's Aladdin.
- Eggman's rambling in STH 204 is likely a Shout-Out to the hybrids in Battlestar Galactica (2003).
- Think again,◊ Sugar-Queen!
- In Issue #103-104, the Freedom Fighters of the Galaxy are modeled after the Guardians of the Galaxy, both written by Jim Valentino. Sonic is Vance Astro, Tailon is Talon, Rotor-27 is Charlie-27, Saleta is Aleta, Bunni is Nikki, Twan-du is Yondu, and Hawkhawk is Starhawk.
- In issue #225, Eggman says, "I love it when a plan comes together!"
- In issue 172, Scourge tells Sonic that all it would take for Sonic to be like him is "one bad day".
- In SSS#5, when the young Freedom Fighters think of a name for their group, Antoine suggests the "Fantastic Five".
- Sonic Universe #29 has Verti-Cal and Horizont-Al singing Scourge a song about how he should always look on the bright side of life. And later on in the issue, Scourge attempts to read a book called How Not To Be Seen.
- Two members of the Sand-Blasters are named "Tex" and "Avery".
- In #234 the newly-roboticised Sally asks Sonic where he was when the brains were handed out, a reference to the SatAm episode "Sonic's Nightmare" in which Sonic dreams Sally was roboticised and she says that to him.
- In memorium to Antonio Prohias, #127 includes a parody of◊ Spy vs. Spy starring Sonic, Knuckles, Eggman, and Shadow.
- In #38, Sonic is humming the Sonic SatAM theme, and wondering where he had heard it before.
- In #76, Sonic and Sally rescues three Mobians resembling three of the mains from Tenchi Muyo!. They show up again in #79, fawning over Elias.
- Sonic Universe #20, Dr. Fukurokov looks at his destroyed machine, muttering "...Inconceivable... inconceivable... inconceivable..." Tales replies "You keep saying that word. I don't think you know what it means.
- Early (and obvious) cracks at The Little Mermaid.
- Julie-Su watching Buffy the Vampire Slayer.
- Rouge "specializes in stealing precious things."
- Crazy Robotnik is a shout-out/meme spamming machine. The most prominent is 2 plus 2 equal 10 ... in base 4 and of course, "snooPING AS usual".
- At the beginning of Knuckles #4, Vector appears to be singing a parody of "Under the Sea"
- The scientist Dimitri is a reference to the creator of the periodic table.
- In Sonic Universe #66 Bean the Duck threw dozens of bombs at a Dark Gaia Titan for insulting his bomb making abilities. It didn't actually, it was a lie made by Charmy Bee to get him to attack it. Bean in his rage actually noted that the Titan didn't have a mouth. When he was dragged away by the other Hooligans he told it to "Find me in the Alps, pal!".
- The old Sonic Universe blog outlined the fate of all the E-100 series robots never seen in the comics proper; there, it was stated that E-117 Sigma infected Gamma with "Zero Viruses" while they were fighting. This is a pretty blatant reference to the Mega Man X series.
- In Sonic the Hedgehog/Mega Man: Worlds Collide #6, Sonic tries to make up new names for his roboticized friends, and is cut off by gunfire when he refers to Charmy Bee/Charmy Man as Blast (Hornet), and Espio/Espio Man as Sting (Chameleon). He also isn't sure what to think of when he sees Vector, because the name "Vector Man" makes him think of a trash-collecting robot.
- All of the events taking place in the Champions arc starting in St H #268 are a shout-out to the 1996 game Sonic the Fighters . Playable characters included Fang The Sniper (who later was redesigned into Nack the Weasel), Bean the Dynamite, Bark the Polar Bear, Knuckles the Echidna, Espio the Chameleon, Amy Rose, Knuckles and Tails. Honey the Cat, although part of the original game, was scrapped, only to return in the 2012 re-release with Dr. Eggman and Metal Sonic.
- One of the fighters Sonic manages to knock out of the running in the tournament was Segata Sanshiro, the old defender of Sega Saturn himself. He gives much respect to Sonic despite the defeat.
- Honey The Cat is a fashion designer much like the character Honey in Fighting Vipers;.
- Amy's clothes come from a fashion line know as The Dream Casters. A reference to the SEGA Dreamcast console and the Dreamcast era which was the time Amy got her current cloths.
- In Issue 270 (Part 3 of Champions) Bean makes a reference to the Mario & Sonic at the Olympic Games series.
Wait... What event is this? Heyyy... That plumber lied to me!
- Phage bears more than a passing resemblance to Arakune, complete with the amorphous squiggly appearance and a creepy mask.
- In the Sonic Boom spinoff, Tails spends his Establishing Character Moment geeking out over Eggman's mech even as he's trying to help destroy it. He asks Eggman at one point what the output of the primary drive is.
Dr. Eggman: Oh— only about 1.21 Gigawatts!Tails: Great Scott! No way!
- The "& Knuckles" variant cover◊ of Sonic Universe #89 has Espio yelling "Why am I connected to the bee?!".
Shout Out / Archie Comics' Sonic the Hedgehog
A list of Shout Outs in the Archie Comics' Sonic the Hedgehog series.