Literature

The title character is name-dropped in Ready Player Two in an off-hand piece of dialogue as a verb.

"Anorak just went Sonic.Exe on us! This is so bad-"

Videogames

Five Nights at Freddy's World: The "Foxy.exe" minigame is quite obviously based of Sonic.exe, bonus points in that Foxy is typically portrayed as the fastest of the franchise's characters.
Five Nights at Sonic's: Clone Sonic sometimes appears to have black eyes with red pupils, similarly like Sonic.exe.
Pizza Tower: While it ultimately doesn't appear in the final game, the SAGE 2019 demo has Snick's Challenge, where Snick (an Expy of Sonic) turns into a floating, spooky version of himself, complete with bleeding red eyes and black schlera, that Peppino must flee from.

Sonic Villains: Sonic.EXE/X is one of the many villains the Prime Dimension Dr. Eggman recruits into his group of villains from alternate realities to destroy his version of Sonic. X's backstory is noticeably different however: while he's usually an Eldritch Abomination created from a gap between dimensions, here he's an incomplete computer virus Eggman worked on during the events of Sonic Forces to use against the Resistance before being locked away behind several firewalls when he was deemed too dangerous and unpredictable to be of use. Unsurprisingly, at the end of the "Ask the Eggman Empire Q&A", when he manages to break out the first thing he does is possess both Cubot and Grounder before massacring everyone alongside Fleetway Super Sonic.

Sonic the Hedgehog Twitter:
- In one tweet, a game gear of Sonic.exe is briefly shown.
- In another tweet, people are told to watch out for black cats, saying no one is immune, with the tweet accompanied by an animation of Sonic turning into Sonic.exe after a pitch-black Big the Cat rushes past him, after which Sonic.exe jumps onto a life monitor and dies.
Supermarioglitchy4's Super Mario 64 Bloopers: Sonic.exe appears in SPAGHETTI.EXE.
The Twitter account for Running With Scissors (the developers of the Postal trilogy) sent out a tweet proclaiming that Sonic.EXE himself had played Postal III.

nkrs200's version of Microsoft Sam Reads Funny Windows Errors has a couple of references towards the creepypasta.
- One sign request in Microsoft Sam reads Funny and Stupid Street Signs THE TENTH states that if Sonic.EXE is sighted, you're screwed. Sam replies "Sonic.EXE? No, thanks!"
- Later on, Funny News Bulletins Season 5 Episode 2 has Ryan himself drop Sonic.EXE's infamous "You're too slow" remark while TheROFL98's Zarvox is making Generic News Reporter "assume the position", to which TheROFL98 calls Ryan out on, due to the video being released well after Halloween. Ryan himself argues that he had to make the reference... before corrupted Microsoft Anna showed up.
- In Microsoft Sam Reads Funny Windows Errors Season 14 Episode 2, one of Sam's error requests take him to Zalgo Island of all places, where he's sighted by a distorted version of Radar Overseer Scotty (which the closed captions refer to as "Scotty.EXE") and undergoes a Freak Out as a result.