These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Mario and Spiderman show up with no warning in Diaries to try to stop Satan, but get killed and are never mentioned again.
Shrek makes at least one appearance in every video from Origins onward, with his face often stretched out and calling Knuckles "Donkey." This is because Knuckle's character here is based on Donkey's voice actor, but he still shows up out of nowhere and leaves just as quick.
Batman popping up from nowhere to say "This is bad" in Origins.
When the S.S. Ikea sinks in Doom Ship, Sonic is suddenly joined by other characters Roger Craig Smith voiced to comment on the destruction. Like Batman, they vanish.
Pandering to the Base: The explanation for how Shadow and Knuckles are brought back into the series after they were supposedly Killed Off for Real, and how Eggman allows a clone of Cream to tagalong with him in Doom Ship.
Special Effect Failure: Very apparent in the series, such as the gun used to move characters appearing in plain sight, all the characters having to be dragged across the maps, and the Garry's ModHUD is seen very often.