He is seen through Mr. Krabs' mirror when SpongeBob tries to figure out how to make Mr. Krabs not see the painted dollar but leaves when Mr. Krabs comes home, telling SpongeBob "you're on your own pal". In "Something Smells," SpongeBob's breath smelled bad and he broke the mirror. Patrick invented his own Universe in "Chimps Ahoy," but SpongeBob thought it was just a mirror. AU SpongeBob's Universe might be the same one Plankton visited in "The Algae's Always Greener."
He also appears in "Squid's Day Off" saying "I will destroy the Krusty Krab!," as the result of Squidward's paranoia that SpongeBob will damage the Krusty Krab. He also gets eaten by a monster in "Ghost Host" as part of a long-string of jokes by the Flying Dutchman to SpongeBob.
His most recent appearance was in an unnamed SpongeBob comic in the Nick Magazine September 2009 issue. In the comic, SpongeBob and Patrick get a treasure map from an elderly sailor. SpongeBob reminds Patrick of the curse that the sailor told them off. When SpongeBob then tells him about what the sailor said, a bubble comes up with Alternate-Universe SpongeBob, Alternate-Universe Patrick, and Alternate-Universe Elderly Sailor reenacting when the sailor giving the map to them. When Patrick denies that even happened, the Alternate-Universe Sailor slaps him and says "Sure I did! Pay attention, sonny!" Then, in the background, Alternate-Universe Patrick is laughing at him and Alternate-Universe SpongeBob is just staring at SpongeBob with a blank expression. Alternate-Universe SpongeBob had a Scottish accent in "Chimps Ahoy."
SpongeBob SquarePants (Clone)
SpongeBob and AU SpongeBob are a lot alike. However, AUSB didn't help SpongeBob in "Wet Painters," and acted more dramatic in "The Algae's Always Greener." Not much is known about this relationship, as AU SpongeBob is a minor character.
Patrick Star (Friend)
AUSB is sort of nice to Patrick, saying his idea was a pretty good idea in the only time they really interacted.
AU Patrick (Best Friend)
AUP is a lot like Patrick, and AUSB is a lot like SpongeBob, so we can assume they are best friends as well.
"You're on your own, pal." to SpongeBob
"Well, I thought it was a pretty good idea." to Patrick
"I'm gonna make you eat those words, Krabs!" to Alternative-Universe Krabs
"Eh, eh, eh..." to Alternate-Universe Plankton
"I will destroy the Krusty Krab" to Squidward
"NO SHIRT NO SHOES NO SERVICE!!!"
"SOILED IT SOILED IT SOILED IT!!!"
Alternate-Universe SpongeBob is arguably the most appeared Alternate-Universe character to appear.
This is probability because he is the Alternate-Universe version of the character with the most appearances to date: SpongeBob SquarePants.
Unlike most Alternate-Universe characters, Alternate-Universe SpongeBob isn't shown to be truly evil (though in "Squid's Day Off," he threatened to destroy the Krusty Krab).
"The Algae's Always Greener" is only episode to feature Alternate-Universe SpongeBob without Main-Universe SpongeBob.