I've finally succeeded in getting my text to fade in and then back out. The problem is that now all my GUItext's, not just the one that I specify, end up having their alpha changed:

#pragma strict
var thoughtText : GUIText;
var fadeIn :boolean;
var fadeOut :boolean;
var shedSeen :boolean;
 
function Start () {
        thoughtText.font.material.color.a = 0;
        fadeIn = false;
        fadeOut = false;
        shedSeen = false;
}
 
function OnTriggerEnter (other : Collider) {
        if (other.gameObject.name == "Shed Thoughts"){
                if (shedSeen == false) {
                        thoughtText.text = "Oh lord";
                        Debug.Log("Fade in");
                        fadeIn = true;
                        yield WaitForSeconds (5);
                        Debug.Log("Fade out");
                        fadeOut = true;
                        shedSeen = true;
                }
        }
}
       
function OnTriggerExit (other : Collider) {
        thoughtText.text = "";
}
 
function FadeIn(){
   if(thoughtText.font.material.color.a<1)
      thoughtText.font.material.color.a += Time.deltaTime;
   else fadeIn = false;
}
 
function FadeOut(){
   if(thoughtText.font.material.color.a >= 0)
      thoughtText.font.material.color.a -= Time.deltaTime;
   else fadeOut = false;
}
 
function Update(){
   if(fadeIn)FadeIn ();
   if(fadeOut)FadeOut ();
}

Any help would be greatly appreciated.