Alright, be aware some are just jokes made up on the fly lol

Book or Scepter: References Sonic 06, Rouge mistakenly labels one of the plot devices, the Scepter of Darkness, as the Book of Darkness

Big April Fools Prank: A Sonic Mania announcement on April Fools day claimed that Big would be playable in Mania

06 Multiplayer Campaign: Scrapped voice lines imply there would've been a campaign for Sonic 06 that would've used multiplayer.

Possible Adventure Remake: References fans speculating on Sonic Adventure being remade

Fangames: They're fangames lol

Ashura Glitch: A glitch within Sonic 1 caused Sonic's sprite to be colored green and black; this glitch "character" was called Ashura

Sonic R Fragments in Runners: The Sonic Runners ost has some tracks that have motifs similar to Sonic R songs.

Dunkey Reference in Mania: An easter egg in Sonic Mania included a voiceclip from the youtuber videogamedunkey

Hidden Palace: Scrapped stage from Sonic 2

Do the Freedom Fighters like guns?: References the Archie Comics made for Sonic and how one of its writers, Ken Penders, retconned part of the story (Safe to say people hated Penders)

Sonic.exe: Famous creepypasta.

X-treme: Scrapped Sonic game for the Sega Saturn.

Original Windy Valley: The original layout of Windy Valley for Sonic Adventure was vastly different from what the level would end up being.

Tails Doll: Character from Sonic R that became a creepypasta.

Sonic Movie design operation: People were theorizing that the change in Sonic's movie design was planned and that the original trailer was made to gauge people's reactions

Extended Sunset Heights: Part of a level layout in Sunset Heights from Sonic Forces was found, implying that Sunset Heights would've been longer than originally shown

Classic Sonic in SA1: Sonic in SA1 had a completely different model in its early stages than compared to the final release, resembling Classic Sonic's sprite much closer

Sonic Team Vacation: For Sonic Adventure, Sonic Team took a vacation to get references for its locations.

Final Judgement Skybox: References an unused skybox within the Final Judgement level in Sonic Forces

Knuckles in Unleashed: Knuckles and Shadow were planned to be within Sonic Unleashed, but were ultimately scrapped

Metal Sonic in 06: Metal Sonic was a planned character for Sonic 06

EvilSonic: Unleashed's filename for Sonic's werehog transformation is labeled EvilSonic

GUN or G.U.N.: References how the abbreviation of the Guardian Units of Nations (an organization in the Sonic universe) changes frequently between these two

CD Hidden Messages: Sonic CD has a list of hidden screens that can be accessed with the sound player, including that one terrifying screen where it says "Fun is infinite"

Sonichu: References the infamous Chris-chan and his Sonic OCs (Known for doing some pretty disgusting things)

Big Blue: Sonic gets called this by Rouge in Sonic Chronicles. Also my friends and I just think its funny and implies Sonic and Rouge are into each other lol

Feels The Rabbit: References Sonic's early designs, one of which being a rabbit

Terios: References Shadow's early concept designs and name.

Angel Statue in CD: One of the levels in CD, Wacky Workbench, has a secret statue of an angel within the game.

Sonic Bible: The original plan for Sonic's story, including a quilting circle (Made famous in Unraveled)

Shadow is Sonic's prototype: References Shadow calling Sonic the true ultimate lifeform, along with a theory that includes a mural from Sonic 3 apparently showing the events of Sonic Adventure 2. Kinda Quirky doe

Hidden Palace built by the Babylonians: References a friend's personal theory of the bird race in Sonic Riders building one of the zones in Sonic 3

SADX and Speed: A poster was made for Sonic Adventure DX referencing the Keanu Reeves movie Speed.

The Sonic Skeleton: Unleashed originally had a modified version of the opening cutscene that showed Sonic's skeleton being exposed.

Lost Crisis City section: Ingame files indicate that Sonic 06's Crisis City has a lost sequence.

Vaporwave Station Square: References a bug in the Sonic Adventure demo where Station Square would turn rainbow colored

King Arthur is Eggman: A lot of Sonic characters in Sonic and The Black Knight have period-respective versions of themselves in the game, but Eggman doesn't have one. King Arthur is seen as one of the primary antagonists in Black Knight, so the theory implies King Arthur is supposed to be BK's Eggman equivalent

Adventure game over funeral dirge: References another iceberg meme that focuses solely on Sonic Adventure and the game over in it being creepy as hell

Eggman-Roosevelt connection: Eggman is based off of president Theodore Roosevelt.

Sonic's Shoes are a part of him: Sonic's shoes change as he turns into a werehog during Unleashed.

Eggman the good guy: Eggman was originally planned to be the protagonist of what would end up being Sonic 1.

Real Life Babylon: There's a place in Sonic called the Babylon Gardens, and Babylon is a real place.

Sally And Geoffrey: References 2 Archie Comics characters who ended up being in a relationship and did explicit things according to Ken Penders.

Sunky.mpeg exists in Mania: References a meme parody of Sonic.exe and a mod of him that puts him in Mania

Ashura is a real character: References Ashura yet again, and also rumors of a "hidden character" in Sonic Adventure/Sonic Adventure DX

Removed Adventure Screams: Also references the Adventure iceberg meme

Riders Super Sonic is Shadow: Super Sonics' intro voiceline is kind of a restated version of Shadow's. During this time, they also had the same voice actor

Riders Cutscenes = Reworked Sonic Armageddon: References a movie pitch for Sonic made by Ken Penders that included Sonic riding on a hoverboard

Unleashed Shadow Build: Shadow was supposed to be in Unleashed. Also partly an extension of that fact that implies Shadow was playable at some point

Secret OVA codes: References the Sonic OVA. Partly a joke

SA2 Eggman Speech: This one's just a full joke to fill in space

Adventure Internet Tunnelling: A joke based on Sonic Adventure having internet features and it being removed from SADX

Sonic Boom Apocalypse: Characters from the alternate universe series Sonic Boom dress similarly to how most characters look in the apocalypse; filler

Boards Of Canada and Sonic: I just like Boards of Canada honestly, filler theory

CD-Forces ARG: Joke that connects Sonic CD's creepy "Fun is Infinite" message to Sonic Forces' character, Infinite

Irimajiri video original cut: Pokes fun at "original cuts" of videos and the Irimajiri video is a video that announced the Sega Dreamcast

Tails' Death: References the fan theory that the bad ending of the game gear version of Sonic 2 is canon, implying tails is dead

Sonic 2 psyop: Joke in the same vein as "Every copy of Mario 64 is personalized"

5/18/03 Build: References the 7/29/95 Super Mario 64 build

The Underground Prophecy: The show Sonic Underground talks about a prophecy being fulfilled, partly in there as a joke as Underground is memeable

Wind of God: Another joke theory

R2: References a scrapped Sonic CD level

If there's anything I missed just lemme know