After defeating the final boss, Modern Tails & Classic Tails are briefly seen discussing something at Sonic's birthday party during the game's last cutscene. What they are talking about differs between the English and Japanese localizations of the game.

In the English version, they said:
Classic Tails: He collects how many? Wow, where does somebody put all those gold rings?
Modern Tails: You know what? I don't know. I keep forgetting to ask.

In the Japanese version, they said:
Classic Tails: You added legs to the plane? What have you done to Sonic's Tornado?
Modern Tails: Yeah... I guess really did go overboard with the legs...
Contributed by ProtoSnake
The autotuned part of Escape from the City Act 1 is the same melody from Sonic the Hedgehog 3's Endless Mine level. In addition, Act 2’s theme contains elements of It Doesn’t Matter from Sonic Adventure 2.
Spoiler:Before fighting the final boss "Time Eater", A conversation takes place, wherein the English version of the game, Classic Tails refers to Classic Eggman as "Doctor Robotnik" before being corrected. This is in reference to the original localized name for the character which has since ceased use.
Contributed by ProtoSnake
After clearing Green Hill Zone with Modern Sonic, he will say, "No stranger then rescuing genies and magic books or saving aliens in a interstellar amusement park." A reference to Sonic and the Secret Rings & Sonic Colors respectively.
The opening cutscene for the Shadow fight in the console/PC version of the game is nearly identical to the opening of Sonic Adventure 2: Battle.
In the original E3 demo for the 3DS version of Sonic Generations, a remix of the Doomsday Zone's theme from Sonic and Knuckles can be heard.
This music is not present in the final game.
When the player leaves the game idle as "Classic Sonic", he mimics the waiting poses from the 16-bit era games.
This includes one wait pose from Sonic the Hedgehog, two poses from Sonic the Hedgehog 2, and one pose from both Sonic the Hedgehog 3 and Sonic 3D Blast.
Contributed by ProtoSnake
Sonic Generations was originally planned to be released on the Wii and DS.
Contributed by noobheadz
When Modern Sonic finishes off his freestyle trick, the finish pose that he strikes resembles Sonic's pose from the cover art of Sonic Adventure on the Dreamcast.
Contributed by ProtoSnake
The remix of "Super Sonic Racing" uses samples of the original Sega Saturn promotional video. This is likely a reference to the fact that the track is from Sonic R, which released on the Sega Saturn.
Contributed by Takahashi2212
Sonic Generations development began after Takashi Iizuka, Sonic Team's Director, realized that there was no anniversary game planned for Sonic's 20th anniversary in 2011. The idea for a tribute game was accepted by Sega and development began.
Contributed by Yoshispacedragon
Cream's "saved" cutscene shows a sign in the background that references Blaze the Cat.
Contributed by marioman3
In Rooftop Run Act 1, the flags of all the countries Sonic visited during Sonic Unleashed can be found in the background during parts of the stage.
Contributed by SonicManEXE
The Sonic Generations level list was conducted almost entirely on fan feedback, unknowingly to the fans themselves. Between the game's development cycle, SEGA (specifically the "Sonic" Facebook page) released a poll back in 2009, along with other unimportant ones, simply asking the reader to list their favorite levels from each Sonic game, leaving fans none the wiser. The most mentioned levels from both fans and some internal employees became the official level list for Generations.
Contributed by TheUpbringer
There is a secret statue room in Sonic Generations. It can be accessed by holding back (Xbox 360) or select (PS3) from the Collection room. Statues are obtained by entering codes originally found in specially marked Sonic Generations merchandise and now freely available online.
Contributed by Funland47
Due to its returning cameo in the background of Radical Highway on the 3DS version, NiGHTS is the only non-Sonic character to appear in Sonic Generations.
Contributed by SilverSupernova
Similar to the missing posters of Ray and Mighty in the City Escape level, wanted posters can be seen of Fang, a recurring character in early Sonic games who debuted in the Game Gear game "Triple Trouble" Bean, and Bark, two characters from the Sonic The Fighters game. The 'Wanted' status could both a reference to them being criminals, and due to the fact that fans often request for these three characters to be put into a new game.
Contributed by PheonixGRX
After finishing Green Hill Zone as modern Sonic, Sonic will mention to Tails that the area seems awfully familiar, with Tails saying "not to me." Green Hill Zone was from Sonic 1, while Tails didn't come into the series until Sonic 2, meaning Tails would have no memory of the area.
Contributed by PheonixGRX
Perfect Chaos' appearance in this game is different to its appearance in Sonic Adventure; in Sonic Adventure, it was a creature made entirely out of water, whereas in Sonic Generations, it has scaly, reptile-like skin. According to an interview with Takashi Iizuka in the Prima Strategy Guide for Sonic Generations, Perfect Chaos' 2011 design is how the team had originally planned the monster; it had had to be changed in Sonic Adventure due to the technical restraints of the Dreamcast.
Contributed by lividd3ad
Mighty The Armadillo and Ray The Flying Squirrel can be seen on missing posters in city escape. The posters state that they've been missing since 1993, the year SegaSonic the Hedgehog was released for arcades, where they were first introduced.
Contributed by RayMonkay
Jaleel White, known for his acting as Steve Urkel in the 90's sitcom "Family Matters", was considered by SEGA to be the voice of Classic Sonic. Jaleel was considered because he had previously voiced Sonic in "Adventures of Sonic the Hedgehog", "Sonic the Hedgehog" (1993), and "Sonic Underground". Sega ultimately decided against casting Jaleel, resulting in a mute Sonic.
Contributed by DidYouKnowGaming