A variation: when they reconvened to do Sonic Unleashed, Pokecapn's band usually referred to this game as "that other game" whenever the subject came up. Not surprising considering the effect "that other game" had on their sanity...
They also refer to the magma-lizard enemies as "Dodongos" or "Thriller lizards" (after the funny dance they do when Silver telekinetically picks them up) and the flying magma enemies are "Fire Keese", after the flaming bat enemies in the Legend of Zelda, in keeping with Medibot's need to make everything fit into some other game's logic.
They dub the Demonic Spider black hole things from End Of The World "Time Dimensions".
They also give Sonic the name Rockman Classic/Rockman Blue, Shadow the name Rockman Charcoal, and Silver the name Rockman Steel / Rockman Chrome.
Mephiles is referred to as Mephistophiles, Satan, or Mephisto.
Referring to Silver's Psychokinesis as "Physics". As a result of their Sanity Slippage they use the word "physics" as a verb.
There's also a playthrough by HellfireComms with NTom64 and Fastest Thing Alive, and as if they didn't sit through enough torture, they've begun anew, with The Helldragon replacing Fastest Thing Alive.
Sega weren't quite ashamed enough to write it out of Sonic canon forever, as evidenced by the appearance of a level and boss fight modeled after it in Sonic Generations, albeit with a major gameplay overhaul.
Early trailers and demonstration videos promised things like a day/night system, multiplayer minigames, and a "free mode" that allowed you to play as any character without storyline constraints. Several functions described in the manual are not actually in the game, including things like the implementation of the Action gauge (it is completely pointless for Sonic and is rather barebones for Shadow and Silver), "maturity" levels for Sonic's custom actions (there are none), and a flight gauge for Omega's hover (he can hover forever, there is no gauge). Most depressingly, code was found for a purchaseable gem that allowed Sonic to relive his glory days of going Super Sonic in-level, rather than just for the final boss. Such a thing was never used until Sonic Colors.
There were originally plans to create a Wii port of this game, but time constraints had them make Sonic and the Secret Rings.