Mr. Krabs (shouting in response to Sandy about why there's only one fast-food restaurant in Bikini Bottom) "...There can be only one, drylander!" (Mr. Krabs is Clancy Brown, who played The Kurgan in Highlander).
Jürgen Kluckert, Krabs' German voice actor, gets his own Actor Allusion. In "Born Again Krabs", when faced with the Flying Dutchman, he calls himself "Benjamin Blümchen", a reference to the beloved German children's character that he had succeeded from the late Edgar Ott.
"SpongeBob's Last Stand" features a song called "Give Jellyfish Fields A Chance", which is a parody of John Lennon's "Give Peace A Chance". The scene that the song plays over is a parody of the music video for "Subterranean Homesick Blues".
The middle of the jellyfishing song has a slight rewrite of The Toyes' Smoke Two Joints (replace "two joints" with "jellyfishing").
Mr Krabs: There are 13 bad words you should never use. Squidward: Don't you mean they're only seven? Mr Krabs: Not if you're a sailor. (chuckles)
In "New Student Starfish", Patrick's climb up the mountain of light bulbs has a brief shout out to The Price Is Right's Cliff Hanger Game, complete with yodeling and lederhosen.
In "The Camping Episode", Spongebob and Patrick end up smashing a guitar and a drum set, respectively. Okay, quite a few Rockers Smash Guitars, so that could be a Shout-Out to any of those bands, right? Fast forward to the episode "Sweet And Sour Squid" where Squidward and Plankton are clearly singing a parody of "Pinball Wizard", and it seems to indicate that at least one writer among the crew is a fan of The Who, meaning that in the Camping Episode Spongebob and Patrick were most likely imitating Pete Townshend and Keith Moon, respectively.
During the tenth anniversary special, Robin Williams asked Patchy if he knew Captain Hook. Granted, this is Robin Williams we're talking about, so that line was likely to have been ad-libbed, but still...
In "Squidbob Tentaclepants," Sandy's teleportation device bears a striking resemblance to Brundle's telepods.
"Bye Squidward! Bye Mr. Krabs! Bye, Squidward." "You said "Bye, Squidward" twice." "I likeSquidward."
The second half of "Squeaky Boots" parodies Poe's "The Tell-Tale Heart", where Mr. Krabs steals the rubber boots he gave to Spongebob and hides them under the floorboards of the Krusty Krab, only to still be driven mad by the squeaking.
In "The Bully", the scene where Flats chases SpongeBob down with a garbage truck is very similar to the climax of Back to the Future Part II where Biff chases Marty down a tunnel in his car - both Biff and Flats are even shown close up and laughing evilly behind the wheel. This would also be a very nice Actor Allusion, as Tom Wilson played both of them.
In "To Save A Squirrel", Sandy uses the phrase "Eat or be eaten" to describe was survival training camp is like.
"Big Pink Loser" has a shout-out to The Adventures of Buckaroo Banzai Across the 8th Dimension, of all things, when Patrick claims that his life's dream is "to defeat the giant Monkey Man and save the ninth dimension", later amending it to "to defeat the little Monkey Man and save the eighth dimension" when SpongeBob convinces him that it might be too hard. The titular "eighth dimension" was a key part of the plot of Buckaroo Banzai, and it also featured a race of villainous aliens who called all humans "Monkey Boy" ("It's not my goddamn planet! Understand, Monkey Boy?").
In "Tutor Sauce", Spongebob accidentally sends Mr. Krabs flying into the background coral due to his reckless driving. Ed, Edd n Eddy fans might think of a similarnote In the the sense of background object interaction ONLY gag in the episode 1 + 1 = Ed in which Ed interacts with the background houses.
From "Missing Identity" after SpongeBob's "BLEEUGH!" (after trying Gary's Snailpo) reaches the Snailpo factory's offices:
The premise of "A Pal For Gary", where Puffy Fluffy is bought from a gypsy and becomes a monster overnight, is modeled after the plot of Gremlins, where an adorable creature becomes a ravaging beast if fed after midnight. Only in this plot, the buyer ignores the seller.
Clams has numerous references to Jaws, including the famous theme.
There's also a reference to Moby-Dick, when Mr. Krabs nails a sandwich to the mast as a reward.
There's also a Jaws reference in "SpongeBob, Sandy, and the Worm," where the citizens are discussing what to do about the titular worm, when an old man who resembles a sailor scratches the wall in the same way the man in Jaws scratched the chalkboard to get everyone's attention. However, he just wanted to know where the bathroom was.
Using "Because they're so darn stupid" as the punchline to a lightbulb joke like SpongeBob does in "Squirrel Jokes" was previously done in Raising Arizona.
At the end of "SpongeHenge", SpongeBob sees the Krusty Krab abandoned and half-buried in the sand and breaks down, a la the ending of Planet of the Apes (1968). His hair and beard make him look like Charlton Heston as well.
In "Fiasco!" Plankton ducks inside a movie theater to evade the cops for stealing a priceless art piece made out of a krabby patty. The movie shown is blatantly The Blue Lagoon complete with the two teen characters about to kiss.
"Feral Friends" features a green orb rising from a volcano and mutating everybody except Sandy into more savage, animalistic versions of themselves. It even has musical themes similar to the orchestral score in Heavy Metal.