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In one of the buildings, there is a piece of paper that states "What I learned in Boating School is...," which is a reference to the episode "No Free Rides."
Block City Wars: Mafia Town
When you unlock the Hot Rod, when you tap on info to upgrade your Vehicle, on the the bottom to paint and customize your Vehicle, the second one is the SpongeBob paint art, the bars on the front have SpongeBob's buck teeth, and on the back right is a picture of Patrick Star.
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.
If the player obtains the element "plankton," one of the quotes said by him will be displayed.
In this online game, a portrait of SpongeBob appears as one of the items the boy can reel out of the water. Also, this online game came out in 1999, the same year that SpongeBob SquarePants premiered. Additionally, this being a Nick.com online game is the reason why they have full rights to use the SpongeBob character, even when the rest of the game has nothing to do with SpongeBob.
A picture of Painty the Pirate can be seen in Stealing the Diamond.
A Magic Pencil appears in the SpongeBob SquarePants 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, an infinite white dimension filled with almost complete nothingness.
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 a reference to the episode "Chocolate with Nuts." During the episode, SpongeBob and Patrick bought bags identical to the "purse of holding". The fail message of "you two looks like could use some patened purse of holding purses" is also a reference when salesman try to sell the bag to Spongebob he said "you two are too smart without my patened candybar bag carrying bag".
There is a character named Paddy Pride in Completing the Mission, which references a YouTube Poop based on the episode, Patty Hype.
In the app game High School Story, there is a mentioned burger place called "Admiral Burger," which seems to be similar to the Krusty Krab because both have a pirate theme to them, a secret recipe, and a competitor that is across the street.
In the online video game Kingdom of Loathing, the player can fight a sponge. One of the messages that displays when it attacks the player is "It smacks you with a piece of its pineapple house. Gah. Who lives in a pineapple under the sea, anyway?", a reference to the theme song. Another reference to the theme song is in one of the messages that displays when it misses, being "It sings its incredibly annoying theme song. You tune it out."
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.
On the online gaming MMOG website Roblox, 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 the Scribblenauts games, the player can type "living sea sponge" as a human, then makes a spatula, which will walk up to the spatula and pick it up.
In the game 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.
In the game Splatoon, there was a Splatfest in April 2016 that is themed around SpongeBob vs. Patrick. The winner of the Splatfest was Team Patrick, having the most wins over Team SpongeBob, which SpongeBob won in popularity.