Who's your hero today? - Me :) - You need to detect the moment you hit the ground with. This little snippet does just that - Just stick this in with the rest of the stuff you got and you should be good to go.

 private var hasJustLanded = false;
 function Update()
 {
      if (controller.isGrounded) {
          if (!hasJustLanded) 
          {
               hasJustLanded = true;
                 Debug.Log("yo I just landed, where you at?");
               // play your extra sound here...
          } 
      } 
      else
      {
         if (audio.isPlaying) audio.Stop();
         Debug.Log("yo check dis out am flyin! :D");
          hasJustLanded = false;
      }
 }

EDIT: Please work on improving your programming skills, I'm asking you this for your own good, you won't go too far without good programming skills, watch/read more tutorials. This should be a simple edit/insert to you previous code.

OK, first things first - I'm gonna assume that you only need 2 clips, one for moving (running sounds for example) and other for falling/landing on the ground. You should make those clips public and assign them via the inspector.

Please excuse my JS syntax, I'm by no mean a JS coder.

pragma strict

 // NEW STUFF
 // Inspector variables
 var moveSound : AudioClip;
 var landSound : AudioClip;
 
 private var hasJustLanded = true; // if you set this to false, the clip will play when you start the game - see the logic below of how this will happen.

 // var isGrounded : boolean = true; what you need this for? - the controller already has that variable defined for it (controller.isGrounded)
 var controller : CharacterController = GetComponent(CharacterController);     
  
 function Start () {
     // by default, let your audio source plays the moving sound
     audio.clip = moveSound;
 }

 function Update()
 {
     var isMoving = Input.GetKey("w") || Input.GetKey("a") || Input.GetKey("s") || Input.GetKey("d");
     if (controller.isGrounded) {
         if (isMoving) {
             if (!audio.isPlaying) {
                 audio.Play();
             }
         }
         else if (audio.isPlaying) audio.Stop();
         if (!hasJustLanded) {
             hasJustLanded = true;
             Debug.Log("yo I just landed, where you at?");
             // play your extra sound here...
             AudioSource.PlayClipAtPoint(landSound, transform.position);
             Debug.Log("BOOM");
         }
     }
     else {
         if (audio.isPlaying) audio.Stop();
         Debug.Log("yo check dis out am flyin! :D");
         hasJustLanded = false;
     }
 }

Wondering about PlayClipAtPoint? It creates an audio source at the position you specify and plays the clip you give it at that position. More info here.

I know the code looks a bit freaky now, but try it out and tell me if it works or not, in the meantime I will try to simplify it for you.