SpongeBob: He dies from eating too many Krabby Patties. It happened to that one guy in Sponge Out of Water...
Patrick: Something stupid, I guess. </squidward>
Squidward: Krabs makes him into calamari to sell at unreasonably high prices. Or choking on a fork laughing at something.
Krabs: The Flying Dutchman, fed up with his countless IOUs, finally takes his soul and puts it in his pickle soul bag. Without a soul, Krabs dies.
Plankton:
-After the movie -- he gets killed by inmates at the Institution for the Criminally Tiny.
-Before the movie -- He gets the formula after Krabs' death, but drops the bottle and it shatters, with a stray glass shard stabbing out his eye. His last words: "Oh, the cruel irony."
Sandy: Dome breaks, squirrel dies. Or choking on an acorn.
Gary: Either starvation or Puffy Fluffy comes back and swallows him whole...
Pearl: Freak breaching accident.
Flats: Dies from exhaustion.
Mrs. Puff: Suffers the same fate as Mr. Puff.
"My Leg!" Guy: Dies from a leg infection. His reported last words were "My leg!"
Squilliam: Dies laughing at the circumstances of Squidward's death.
Flying Dutchman: Some exorcist fish (exor-fish?) exorcises him. "THE POWER OF NEPTUNE COMPELS YOU!"