Help Wanted / Reef Blowers / Tea at the Treedome - S1-E2
Trivia: In the episode "Help Wanted", Spongebob has a pet flying scallop in a cage hanging from the ceiling in his room. It is never seen again in the entire series.
The Sponge Who Could Fly (aka The Lost Episode) - S3-E16
Trivia: The miner who gives Patchy the video tape is Stephen Hillenburg, the creator of SpongeBob SquarePants. (00:04:53)
The Nitwitting/The Ballad of Filthy Muck - S12-E2
Trivia: In "The Ballad of Filthy Muck", there's a citizen that reads the newspaper headline that has an overly-large nose. His speech pattern and caricature nose is impersonating Jimmy Durante.
Spy Buddies / Boat Smarts / Good Ol' Whatshisname - S5-E4
Trivia: At the end of "Spy Buddies", Plankton gives Mr. Krabs $1, as part of the usual bet. This is a reference to "Trading Places", where the Duke brothers' usual wager was $1.
The Bully / Just One Bite - S2-E17
Trivia: In "Just One Bite", there was a deleted scene where Squidward enters the Krusty Krab at night. Squidward opens the door, and a bucket of gasoline falls and spills all over the ground. A robotic arm drops a lit match to light the gasoline.
Trivia: For an unknown reason, the opening credits of both episodes are a lighter blue than usual.
Answer: I believe this is the Season 6 episode "Spongicus".