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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.
Infiltrating the Airship
One of the options in the game is "Magic Pencil". If chosen, Henry will draw a wierd creature on the ground, which comes to life and hits him. This is a reference to "Frankendoodle."
In the online video game Kingdom of Loathing, you can fight a sponge. One of the messages that displays when it attacks you 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.".
One of the splash texts that comes up on the home page says "Lives in a Pineapple Under The Sea!", a reference to the SpongeBob theme song.
Plants vs Zombies
In Plants vs. Zombies: Garden Warfare, there's 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 Website Roblox, the official Roblox made a mini Invincibubble that you can put on your character's shoulder. It is no longer available since it was specially released for Sponge Out of Water.
In the Scribblenauts games, you can type 'living sea sponge' as a human, then makes a spatula, it 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.
Snail Bob 2
Snail Bob has a picture of Gary in his house, with the caption "Cousin Gary."
One of the enemies that can be fought looks similar to Gary.
In the game Splatoon, there was a Splatfest in April2016 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.