- Tails not remembering having ever been in Green Hill Zone, since he wasn't in the series yet.
- This game's version of Green Hill Zone has an expansive, flooded underground area, similar to the Master System/Game Gear version of the first Sonic game.
- Near the beginning, Sonic makes a call back to the Secret Rings and Sonic Colors in the same sentence:Tails: This place looks like something sucked out of life and color of it. Totally strange.
Sonic: No stranger than rescuing genies in magic books or saving aliens in an interstellar amusement park.
- At one point Sonic repeats a line almost directly from Sonic Colors:(In Colors) Cubot: "Your plans have been crushed by Sonic for, like ever. He stops you like it's his job or something."(In Generations) Sonic: "Seriously, we beat this guy every time. It's like it's our job or something."
- Almost every supporting character is rescued in a stage they had some previous connection to:
- Knuckles in Sky Sanctuarynote
- Amy's case is unexpected: While she is featured in Chemical Plant, the boss race against Metal Sonic in Stardust Speedway follows after that level, and Amy originally needed to be rescued from there.
- Rouge in City Escapenote
- Cream & Cheese's appearance in Speed Highway is unusual: Cream makes a cameo appearance in Sonic Adventure DX, which was released near the time of Sonic Advance 2, her first appearance in the franchise. However, Cheese is a Chao and the first debut the Chao made were in Sonic Adventure.
- Espio in Seaside Hillnote
- Blaze in Crisis Citynote
- Charmy in Planet Wispnote
- At the end of the game, it is revealed that Generations is the direct sequel to Sonic Colors. To be more precise, Eggman explains that he found the Time Eater immediately after The Stinger of Colors.
- In the English pre-final boss cutscene, Classic Tails refers to Classic Eggman as "Dr. Robotnik", then Classic Eggman corrects Classic Tails, stating that nobody calls him by his real name anymore.
- Modern Sonic first gets a tutorial on Light Dashing in Speed Highway — Sonic Adventure was the first game to give Sonic that ability. On the same note, the first tutorial on walljumping is in Seaside Hill, which gave the 'speed' member of each teamnote a walljumping ability — including Sonic.
- In the 3DS version, Classic Sonic learns how to Homing Attack in Emerald Coast, which hails from the game where he first displayed that ability.note
- After the credits, Classic Eggman and Modern Eggman are arguing when Classic Eggman asks "Do we ever win?", Modern Eggman responds "That depends on your definition of 'win'". As Eggman did win in Sonic Riders, but he only won a carpet.
- A subtle one occurs within the levels. The springboard from Sonic the Hedgehog 2 appears in this game, in Classic Sonic's stages. What should be noticed is that Green Hill Zone (the level from Sonic 1) is the only level that doesn't seem to have them, while it was introduced in Chemical Plant (the level from Sonic the Hedgehog 2).
- There's also a small one in the cutscene where Sonic finds Knuckles — who immediately performs a watered-down version of the Spiral Upper upon being unfrozen.
- Upon being rescued, Blaze jump up through the scenery of Crisis City, resting at it's peak before returning to Sonic. Clearly a reference to Silver's introductory movie in Sonic 2K6 where she is seen rooftop hopping in a similar fashion.
- Noticeably, while the level design is new, the levels reuse some elements from the original levels. Levels from the Genesis levels start exactly the same way as they did in the original games before straying for a new level design when playing as Classic Sonic, while the Dreamcast and Modern levels do the same when playing as Modern Sonic.note
- Tails notes that Chemical Plant's purple water "makes him nervous for some reason". This is because in the original, said water would start rising at some point, and unless Sonic outran it, he would eventually drown. Tails' discomfort references how even Sonic Team admitted that said level was too hard for that point in the game.
- Crisis City spawned the "That tornado is carrying a car" meme and in the 2006 version, Sonic is running away from it. Generations sort of makes fun of this in two ways. In Act 1, Classic Sonic must hop through the floating platforms, some of which are cars. In Act 2, Modern Sonic is running towards the tornado. Three guesses as to what he's being attacked with, and the first two don't count. The achievement for running towards it without being hit further lampshades this.
- The cutscene prior to the battle with Shadow has Sonic and Shadow mimicking the updated opening for the Gamecube version of Sonic Adventure 2 (Battle).
- Sky Rail's propeller Springs can be found in one of Sky Sanctuary's challenges.
- Before the game was released, SEGA used the original blue-text-on-white-background logo, complete with "SEEGAA." It was changed to the newer one in the full game.
- In Act 1 of Sky Sanctuary, there are platforms that allow Sonic a small degree of flight when he runs across them, similar to the tops from the Marble Garden Zone of Sonic the Hedgehog 3.
Continuity Nod / Sonic Generations