Karen's "kissy face" screensaver from "Grandmum's the Word" reappears when she is kissing Plankton.
When Squidward turns on the Krusty Krab's security footage, a drawing of DoodleBob can be seen on the bottom of the table.
SpongeBob mimicking Plankton is a reference to "Mimic Madness."
Plankton turning into a genie when he is trying to open the Krabby Patty formula is a reference to "Spin the Bottle."
Squidward's claustrophobia from "Wishing You Well" is brought up again in the ending.
The boot that squishes Squidward is similar to how The Cyclop's Bigger Boot squishes Dennis from the first movie.
Squidward getting tortured by fire is similar to the deleted scene from Just One Bite
The piano falling on squidward is similar to Spongebob dropping a piano on Plankton (Dr. Peter Lankton), twice, from Fear of a Krabby Patty.
This episode confirms the theory that Plankton and Karen live in the Chum Bucket and even have their own rooms.
When Squidward turns on the Krusty Krab's security footage, the date 05-01-99 (May 1, 1999) can be seen on the bottom of the table. This is a reference to the airdate of "Help Wanted," the SpongeBob SquarePants first episode.
Cultural references
The boat that fell on top of Squidward is the RMS Titanic, a British passenger liner that sank in the Atlantic after colliding with an iceberg on April 15, 1912.
