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).
"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 immitating 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."
"Karate Island" is one long shout out to Game of Death, complete with Sandy wearing the famous yellow tracksuit Bruce Lee wore in said movie.
If it's SANDY dressed like that, it could be a shout-out to a shout-out, i.e. Kill Bill.
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.