(Spoiler: There is a lot more than i can say)
Tails scream from the MSTCrimson Sonic.Exe game is played during Tails jumpscare portion albeit more high pitched
The Drowning theme is used as a leitmotif during the portion after Tails, likley refrenching its the theme Sonic used when chasing Tails.
Knuckles theme is the instrumental for the large portion of his part in the song.
Giorno's Theme plays during Knuckles part as well
Reference to Fierce Battle (Mostly known as Mecha Sonic's theme) plays during another of Sonics portion, which in turn is a reference to them referencing fierce battle before in You Can't Run (I honestly can't blame you if you couldn't understand what i just typed)
Phantom notes appear during Knuckles part of Triple Trouble referencing how Sonic did the "Nothing personal kid" maneuver on Knuckles.
Endless is a leitmotif.
Robotoniks Theme plays during his part as a Leitmotif.
Don't know if this counts as a "Reference" but Tails singular eye is supposed to look like a Red Ring.
Bro i need to touch grass
This isn't even all of them