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.
Remember in Sonic Adventure where Sonic says, after every boss fight (even Perfect Chaos), "Hey, I'll play with you some other time."? Well guess who's the boss for the Dreamcast era.
When Rouge and Shadow appear to cheer Sonic on before fighting the Time Eater, Classic Eggman asks who they are, since he hasn't met them yet.
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 except Team Rose a walljumping ability — including Sonic.
In the 3DS version, Classic Sonic first learns how to Homing Attack in Emerald Coast — Sonic Adventure.
The final boss is revealed to be a creature having turned manned machine by the combined efforts of Classic and Modern Eggman, which makes sense when you remember all the classic Mooks Eggman built were powered by animals he captured.
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.
This is followed up by Classic Eggman considering going for a teaching degree, a possible nod to Sonic's Schoolhouse, in which he appears.
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 preforms 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 Crisis City is the only level that doesn't do this, however.
The game even goes out of its way and lampshades the series' Nightmare Fuel as well, when Tails notes that Chemical Plant's purple water "makes him nervous for some reason". note This is because in the original, said water would start rising at some point, and unless Sonic outran it, he would eventually drown in it. The scariest part in this being, of course, the series' infamousScare Chord-ish "drowning music" that signals whenever a playable character is running out of air.
Tails' quote also lampshades the original Chemical Plant's That One Level status in Sonic 2, which makes sense, especially when you take into account the fact that even Sonic Team themselves had trouble beating it.
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.