It could be "Das Bus" or "Treehouse of Horror V".
In "Das Bus", a busload of kids from school went missing and ended up as castaways on an island (a. la. Lord of the Flies).
In "Treehouse of Horror V", students were going missing (and their absence from class was noticed by other students, such as Lisa and Bart) because the teachers were serving the students as food in the cafeteria.
A little more information would help in narrowing down which episode you've got in mind.
