Mainstream continuity
The mainstream continuity contains all characters seen in the SpongeBob series. It is seen in every episode
"Mr." Plankton continuity
First seen in The Algae's Always Greener and probably divergent off the flashbacks in Friend or Foe, this universe has a Plankton that made the Krabby Patty formula accidentally, leaving a nudist (probably from insanity) Krabs trying to steal the formula. Everyone in that universe alive at its creation/diversion had the same memories as their mainstream counterparts did until that point. Plankton, now named Mr. Plankton, married the mainstream Pearl's mother and had an alternate Pearl with her. He also hired the likes of the loyal SpongeBob and the complaining Squidward. One day, when that universe's Plankton probably went out of town, the mainstream Plankton took his place for a few hours just to see what life was like for Mr. Krabs. He did not do a good job. He gave that universe's Pearl only $1.00 for her allowance, switched SpongeBob's and Squidward's jobs around, did nothing to stop Mr. Krabs from getting the formula, and only two Krabby Patties that were in his office and his success that he temporarily had. After seeing through that universe's Krabs how annoying he really was, he went back to the mainstream continuity and that universe hasn't been seen since.
White Pocket Dimension
Most likely existing outside the multiverse, and first seen in SB-129, no one has a clue how this universe came into existence. It is void of any confirmed life and anything but colored squares and voices only known to say "alone." The mainstream Squidward, when escaping a primitive sponge and starfish millions of years into his past, accidentally accessed a glitch in his time machine. He broke of the switch and appeared a few minutes later in the void. He liked the solitude initially but got so lonely, he pleaded the mentioned time machine to go back to his reality.
Patchy's reality
The world that Patchy lives in. SpongeBob is just a character in fiction and does not exist. It is seen in every episode with Patchy, and presumably Neptune's Spatula and I Had an Accident.
"Goneverse"
In this universe, SpongeBob is gone. It proves that SpongeBob is a very important factor of Bikini Bottom. It is seen throughout the shorts all known as What if SpongeBob was Gone?.
Two Mainstream continuities?
In most multiverses, there are two mainstream continuities, each containing opposite truths to the other. There are certain episodes that contain opposite truths such as Something Smells, and Rule of Dumb against Big Sister Sam. Pre-Hibernation Week, Squid on Strike, Shell of a Man, Mrs. Puff, You're Fired and Roller Cowards against Plankton, Squidward the Unfriendly Ghost and Squirrel Jokes. Others have conflicting truths.
Non-canon universes
Battle for Bikini Bottom
Plankton made robots to help him rule the world. However, that didn't work as planned and they disobeyed him because of one flaw. He made several somewhat small robots, somewhat bigger robots, even bigger robots and robots at least 30 times the size of their basis (Sandy, Patrick, SpongeBob and himself). SpongeBob struck a deal with Plankton and fought robots, King Jellyfish, Prawn and the Flying Dutchman to get Golden Spatulas to thus get in the Chum Bucket. Once there, he fought a robot version of himself and Plankton. Once the robots were defeated, everyone went back to their regular lives.
Nicktoons crossovers
Lights, Camera, Pants! (Console)
Gill Gilliam is trying to make a The New Adventures of Mermaidman and Barnacleboy and is having trouble. He asks SpongeBob, Patrick, Squidward, Mr. Krabs, Plankton and Sandy to help him make the new show by competing with each other in 30 matches to see the who fit the role.
Lights, Camera, Pants! (PC)
Like the above, Gill Gilliam is hiring roles for the same shows but gets more than the above for options.
The Endless Summer
Mr. Krabs decides that to make more money, he needs to make a pool and the surrounding enviroment to be very hot. However, SpongeBob makes it hotter and eventually, everybody in Bikini Bottom evacuates except SpongeBob and Mr. Krabs.