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In one of the coloring pages, a beady-eyed starfish wearing green swim trunks with purple spots lies on one of the ocean floors.
Danganronpa V3: Killing Harmony
Tenko asks Keebo if he would be "stuck living under the sea, beneath a rock or in a pineapple?" when he explains he would sink into water. This is referring to Patrick and SpongeBob's respective residence.
A Magic Pencil appears which is a reference to the episode "Frankendoodle," and is an option in Infiltrating the Airship and the laser-cut option fail quote is a meme from the episode "Sandy, SpongeBob, and the Worm."
Also in the game, during the teleporter fail, Henry is teleported into a huge white void where nothing is present. The teleporter also malfunctions, making it hard for him to go back. This is most likely a reference to "SB-129," where Squidward used a time machine, only to end up in Nowhere.
During the Diversion scene in the "Triple Threat" route in Completing the Mission, there's one Toppat Clan member doing Mr. Krabs' iconic robot dance from the episode "Krab Borg."
During the Capital Gains route, there is a option call "Purse of Holding". This is likely a reference to the episode "Chocolate with Nuts."
A sponge can be fought. A message that displays when it attacks "It smacks you with a piece of its pineapple house. Gah. Who lives in a pineapple under the sea, anyway?" as well as a message that displays when it misses "It sings its incredibly annoying theme song. You tune it out." are both references to the SpongeBob SquarePants Theme Song.
In Plants vs. Zombies: Garden Warfare, there is a map called "Driftwood Shores," which has multiple stores that have a sign that says "Porous Bob's" with a sponge logo design. The sign also says that Porous Bob's sells scuba supplies, a reference to the location of the series, and neck ties, an item of clothing that SpongeBob is regularly seen wearing.
Roblox officially partnered up with Nickelodeon and made a mini Invincibubble shoulder pal that the player can put on their avatar's shoulder. There was also an Invincibubble hat that the player could wear on top of their avatar's head. It is no longer available since it was specially released for The SpongeBob Movie: Sponge Out of Water.
In Scribblenauts, the name "living sea sponge" can be typed as a human and can make a spatula, which can also be picked up.
In Scribblenauts Unlimited, there is an easter egg from Lost Kingdom of Parentheses that has a rock, a tiki mask, and a pineapple. Tapping on them and pressing 'use' will spawn a starfish, a musical squid, and a sponge respectively.