"Fear of a Krabby Patty" has a scene in which Squidward tells Mr. Krabs he has to go home because he's SO tired, the bags under his eyes have bags under the bags. Cue a Gross-Up Close-Up with a woman shrieking rather appropriately in the background.
"SB-129": Squidward ends up in prehistoric Bikini Bottom and comes across Spongegar and Patar. Patar greets Squidward with a Gross-Up Close-Up of his mangy grin, bearing teeth and gums and exuding halitosis.
"The Splinter": SpongeBob gets a splinter at work. Rather than making the best of this sure-to-be-disgusting plot and having him try to get it out in a silly fashion, we're treated to 11 minutes of it getting infected, swelling, and oozing pus all over the place until Krabs walks up and pulls it out, thus causing gallons and gallons of puke green pus to shoot out and cover everyone.
In "Plankton's Regular", SpongeBob (via getting pushed under a door) and Plankton (via force-pulling) both are peeled, quite disgustingly.
In "House Fancy", Squidward loses a toenail in the grossest way he can. Squidward gets the leg of a couch on his toe, and it's ripped off by SpongeBob pulling the couch away too soon. It had blood and veins still attached, even. To make it all worse, Squidward slips on the bloody nail. You want to see it? Here you go.Have fun.
"To Love a Patty", SpongeBob falls in love with a Krabby Patty, keeps it around until it's moldy, fungus-covered and maggoty, then eats it. It had maggots, worms, blue and black mold, highly detailed rotten meat, and an assortment of other disgusting things that you could imagine painted with incredibly uneeded detail. See for yourself◊ A similar plot had Krabs not wanting to dump a moldy patty so he can make money off of it. Apparently hospital visits cost less than a patty.
The episode where SpongeBob adopts a worm and it has babies, which he then tries to get other people to adopt. Normally worms are fine in the series, but for this episode? They purposely made them incredibly disgusting. It was horrible.
An episode featured Patrick tearing the entire front half of his skin off, revealing his bones and organs underneath, after a misunderstanding; SpongeBob looks suitably grossed out. It's kind of tame compared to most of the examples in this list (and definitely tame compared to "The Splinter"), but it could still cause instant gag reflexes in some.
"SquidBob Tentaclepants": SpongeBob and Squidward were accidentely fused togther. Most of it wasn't so bad, but at the very end, when they were finally separated and Squidward wanted to be fused together again for personal gains, he accidently caused not just SpongeBob but several other characters to be fused together as one huge fleshy blob! Uggghhh.... and this is a kid's show for crying out loud!
Squidward: It all started...when I was born.
This scene was actually cut out in some countries, leaving the episode with No Ending.
"The Donut of Shame". Patrick gets a donut he believes is SpongeBob's but keeps wondering if he should eat it or not. So throughtout the episode, he does a lot of things including placing it in a couch, a toaster, a toilet, and his own butt (seriously). Then twice he eats it and pukes it back up. At the end of the episode, SpongeBob EATS it. If you look closely, you can see SpongeBob's look of horror as he "savors" the donut.
SpongeBob — as a fetus — eating a Krabby Patty — through his ''umbilical cord — in his mom's womb in "Truth or Square". The notion isn't particularly bad... it's the presentation. The Krabby Patty travels through the umbilical cord, and it's pretty straight-forward, until SpongeBob rips the umbilical cord out of his abdomen and puts it in his mouth to suck it like a straw!
"Pineapple Fever" has Squidward rip his own eyebrow (WITH the skin) off after SpongeBob makes a loud noise.
The episode where Krabs and Plankton compete by selling more greasy items (including "soup" which is just grease on a plate).
The episode where Plankton hides out in a machine designed to look like a milkshake, and is then drank by a fish. Guess how he gets out.
An episode had Squidward giving Mr. Krabs a massage, and lowers his shirt to find it full of barnacles with insects crawling over it.
Patrick eating a rancid piece of Krabby Patty that was in his belly button.
The Plankton Show has a lot of these but a list would be too long.
"For Here or to Go" has Plankton winning a Krabby Patty after a seed counting contest. Most of it wasn't so bad until the end. He has to eat it and digest in the restaurant, and then he goes to the Chum Bucket for Karen to use a sawblade to get it out of his system. The worst part? NO ANESTHETICS! At least it was offscreen.
After that, Karen "jokingly" puts Plankton's body fluids in his Krabby Patties. We even get a Gross-Up Close-Up of the bag it's in!
The scene of Spongebob cutting the huge zit off of his nose with a large pair of scissors in season 2's "Krusty Krab Training Video." Just.... Deuueaugh.
In "Free Samples", after eating a Krabby Patty, two fishes' heads morph into hands that high five each other.
In "Eek, an Urchin!", the urchin lands in the Krusty Krab dining area. The customers, completely oblivious to the urchin, proceed to choke on and eat it.
And Gary's vein exposed pulsating skin after his shell is broken.
All of the "funny" faces in "Face Freeze!".
In "Giant Squidward", Squidward is forced to have a bunch of boy scouts sleep under his toenails. It's pretty tame compared to most of the examples of this page, but it's still pretty gross in context.
The entirety of "The Gift of Gum". Basically, Patrick gives SpongeBob a gigantic ball of used gum. It's as disgusting as you would think.
Brain Gary from "The Inside Job".
Which is lampshaded by Plankton immediately afterwards.
Plankton: That's disgusting!
In "Suction Cup Symphony", Patrick breaks his bones in his butt and it causes them to be visible outside. So he pushes them back inside, and briefly you can see the bones inside his mouth. Uggghhh...
In "Mermaid Man and Barnacle Boy IV", the shrunken residents of Bikini Bottom enter Spongebob's body, via his pores, and continue to attack his innards, most notably, Squidward taking a saw to a vein.
In "Squid Baby", where Spongebob had to change Squidward's dirty diaper. We even get close-ups of the dirty diaper. Soon after Squidward bumps his head in the ice machine he is back to normal. He discovers he is wearing a dirty diaper (even a "fart" is heard when he opens up the diaper). It's just disturbing.
In "Little Yellow Book", Patrick is in a dumpster when he finds a ketchup packet and says that it'll go great with an old diaper.
People who have Trypophobia are advised to NOT watch "The Monster Who Came to Bikini Bottom". You will be thankful you hadn't.