Multiple file creation with sorted input
Formatting

Your if statement block should use braces { ... } to better identify the scope of each clause as a good practice. Also, you can consider renaming setgpa(double)/getgpa() to setGpa(double)/getGpa() respectively.

try-with-resources

Since Java 7, you should be using try-with-resouces for safe and efficient handling of your I/O resources:

private static final Path HONORS = Paths.get("Honors.txt");
private static final Path GOOD_STANDING = Paths.get("GoodStanding.txt");
private static final Path PROBATION = Paths.get("Probation.txt");
private static final String DELIMITER = ",";
private static final int QUIT = 999;

public static void main(String[] args) {
    try (PrintWriter honorsWriter = new PrintWriter(HONORS.toFile());
         PrintWriter goodStandingWriter = new PrintWriter(GOOD_STANDING.toFile());
         PrintWriter probationWriter = new PrintWriter(PROBATION.toFile());
         Scanner scanner = new Scanner(System.in)
    ) {
        // ...
    } catch (IOException e) {
        throw new RuntimeException(e);
    }
}


I have taken the liberty to declare your file paths as private static final constants outside of the main() method, again as a good practice. Also, I have opted to use a PrintWriter, which is buffered, so that I can make use of its println(String) method.

Determining the student's details and ranking

You are creating only one Student instance, and then repopulating its details for each input. Ideally, you should be creating a new one each time, so that they can all go into a Collection in the future for further processing. Right now, you probably can settle for temporary variables in order to print them afterwards.

Assuming we are sticking with your approach, you can hide the Student creation within its own method, e.g. getStudent(Scanner). The idea is that given a Scanner instance, student details can be retrieved and a Student instance is returned:

Student student = getStudent(scanner);


Joining strings with delimiter

Since Java 8, you can use String.join(CharSequence, CharSequence) to easily join strings:

private static String toFileOutput(Student student) {
    return String.join(DELIMITER,
            Integer.toString(student.getID()),
            student.getFirstName(),
            student.getLastName(),
            student.getGpa());
}


Determining the file output

Instead of reassigning the writers to a writer, you should be using them directly:

Student student = getStudent(scanner);
while (student.getID() != QUIT) {
    String output = toFileOutput(student);
    if (student.isHonors()) {
        honorsWriter.println(output);
    } else if (student.isGoodStanding()) {
        goodStandingWriter.println(output);
    } else if (student.isProbation()) {
        probationWriter.println(output);
    }
    student = getStudent(scanner);
}


for vs while

Another way of looping through each Student input is to use a for loop, this approach is sometimes (often? always?) recommended to reduce the scope of the student instance:

for (Student student = getStudent(scanner);
     student.getID() != QUIT;
     student = getStudent(scanner)) {
    // ...
}


Shortening the process

Alternatively, you can consider Files.write(Path, Iterable, OpenOption) to expressively write (pun unintended) a line of output, the only thing to be aware of is that you will need to turn your single String into an Iterable, e.g. using Collections.singleton(T).

Putting it altogether:

public static void main() {
    try (Scanner scanner = new Scanner(System.in)) {
        for (Student student = getStudent(scanner);
             student.getID() != QUIT;
             student = getStudent(scanner)) {
            Set&lt;String&gt; output = Collections.singleton(toFileOutput(student));
            if (student.isHonors()) {
                Files.write(HONORS, output, APPEND);
            } else if (student.isGoodStanding()) {
                Files.write(GOOD_STANDING, output, APPEND);
            } else if (student.isProbation()) {
                Files.write(PROBATION, output, APPEND);
            }
        }
    } catch (IOException e) {
        throw new RuntimeException(e);
    }
}