Controlling the LED by sending Y or N over the serial connection.

serial-led.ino

void setup() {
  Serial.begin(9600);
  pinMode(13, OUTPUT);
  digitalWrite(13, LOW);
  Serial.println("Y for on, N for off.");
}

int ledOn = 0;

void loop() {
  int instruction = 0;
  while (Serial.available() > 0) {
    instruction = Serial.read();
    if (instruction == 89 && ledOn == 0) {
      ledOn = 1;
      digitalWrite(13, HIGH);
    }
    else if (instruction == 78 && ledOn == 1) {
      ledOn = 0;
      digitalWrite(13, LOW);
    }
  }
}