I would make the clues script itself handle this, and use a simple static counter variable to count the number of clues remaining to be found.

Here is the modified script - only a few lines added:

private static var numRemainingClues = 0;
private var shown = false;
var noteText : String = "";

function Start() { 
    // each clue counts itself when it starts:
    numRemainingClues++;
}

function OnGUI() {
    GUILayout.BeginArea (Rect((Screen.width/2)-50, (Screen.height/2) , 300, 300));
    GUILayout.Label(noteText); 
    GUILayout.EndArea ();
}

function OnTriggerEnter( other : Collider ){
    noteText = "Clue Text";
    // each clue counts itself out when shown for the first time:
    if (!shown) {
        shown = true;
        numRemainingClues--;
        if (numRemainingClues == 0) {
            PlayTheDoorAnimation(); // however you want to trigger that
        }
    }
}

function OnTriggerExit( other : Collider ){
    noteText = "";
}

One method is to keep an array of clues found and then opening the door when the length of the array is greater than 4 or something. You can search the array to make sure that the clue isn't already in it and then use the Array.Push method to add a clue id onto the array. e.g.

var cluesArray;

function Start(){
   cluesArray = new Array();
}

function AddClue(clueID:int){
   var alreadyIn = false;
   for(i=0;i<cluesArray.length;i++){
      if(cluesArray[i]==clueID){
          alreadyIn = true;
          break;
      }
   }
   if(!alreadyIn)
      cluesArray.Push(clueID);
   if(cluesArray.length>=4)
      doorOpen = true;
}

Alternatively if there are only a few clues in a place you can use boolean values associated with each clue and only open the door when all clues are set to true. e.g.

var clue1found = false;
var clue2found = false;

function Update(){
   if(clue1found&&clue2found){
      //open door
   }
}

The last sample tells the collider that triggers the event IS the First Person Controller, so it searches an animation in it, but I figure you already know that by this time, don't you ? Instead of using the "other" object, use the door object.

Okay here's the code I got so far:

private static var numRemainingClues = 0;
private var shown = false;
var noteText : String = "";
var other : GameObject;

function Start() { 
    // each clue counts itself when it starts:
    numRemainingClues++;
}

function OnGUI() {
    GUILayout.BeginArea (Rect((Screen.width/2)-50, (Screen.height/2) , 300, 300));
    GUILayout.Label(noteText); 
    GUILayout.EndArea ();
}

function OnTriggerEnter( other : Collider ){
    noteText = "Clue Text";
    // each clue counts itself out when shown for the first time:
    if (!shown) {
        shown = true;
        numRemainingClues--;
        if (numRemainingClues == 0) {
            other.animation.Play("DoorOpen"); // however you want to trigger that
        }
    }
}

function OnTriggerExit( other : Collider ){
    noteText = "";
}

I have the other GameObject var set to the Door in the Inspector for all of the clues, however when I walk into a clue I get the error "Missing Component Exception: There is no animation attached to the "First Person Controller" game object, but a script is trying to access it." I am completely baffled as to why the script is looking for animation on the FP controller.