How Do I Add An Instantiated Object To An Array?

Adding to a UnityScript array is as simple as:

 cubes.push(OBJECT);

Use .NET generic lists. Lots of posts on Lists. Here is a link that includes some information on many of the collection types used in Unity:

http://wiki.unity3d.com/index.php?title=Which_Kind_Of_Array_Or_Collection_Should_I_Use%3F

At the top of the file you will need:

 import System.Collections.Generic;

Then you will declare your variable:

 var cubes : List.<GameObject> = new List.<GameObject>();

Then you can add them to the list with:

 myList.Add(thingToMake.gameObject);

Note if you tag all of your cubes, you can use GameObject.FindGameObjectsWithTag() to get a current array of game objects with that tag. It is a bit less efficient than maintaining your own list, but it is fast enough to use every frame for any reasonable number of cubes.

Thanks for the help everyone! I actually ended up doing it this way:

 #pragma strict
 var timer : float = 0.0;
 var spawning : boolean = false;
 var prefab : GameObject;
 var spawn1 : Transform;
 var spawn2 : Transform;
 var spawn3 : Transform;
 var spawn4 : Transform;
 var spawn5 : Transform;
 //var cubes : GameObject[];
 var board : GameObject[, ];
 var boxColor : Color[];
 private var count : int = 0;
 private var color : int;
 function Start()
 {
     //cubes = new GameObject[40];//[max no of cubes]
     board = new GameObject[5,8];//[x,y]
     count =0;//just making sure this starts at zero
 }
 function Update () {
  //check if spawning at the moment, if not add to timer
      if(!spawning){
           timer += Time.deltaTime;
      }
  //when timer reaches 2 seconds, call Spawn function
      if(timer >= 2){
           Spawn();
      }
 }
  
 function Spawn(){
      //set spawning to true, to stop timer counting in the Update function
      spawning = true;
      //reset the timer to 0 so process can start over
      timer = 0;
      
      //select a random number, inside a maths function absolute command to ensure it is a whole number
      var randomPick : int = Mathf.Abs(Random.Range(1,6));
      
      //create a location 'Transform' type variable to store one of 3 possible locations declared at top of script
      var location : Transform;
      
      //check what randomPick is, and select one of the 3 locations, based on that number
      if(randomPick == 1){
           location = spawn1;
           Debug.Log("Chose pos 1");
      }
      else if(randomPick == 2){
           location = spawn2;
           Debug.Log("Chose pos 2");
      }
      else if(randomPick == 3){
           location = spawn3;
           Debug.Log("Chose pos 3");
      }
       else if(randomPick == 4){
           location = spawn4;
           Debug.Log("Chose pos 4");
      }
       else if(randomPick == 5){
           location = spawn5;
           Debug.Log("Chose pos 5");
      }
      
      //create the object at point of the location variable
      //thingToMake is just a temporary variable to hold our cube 
      var thingToMake : GameObject = Instantiate(prefab, location.position, location.rotation);
      thingToMake.renderer.material.color = boxColor[color];
      color = Mathf.Abs(Random.Range(0, boxColor.Length));
      //put elements in arrays
      //store cubes in "max" and this will allow us to run checks against their color or any other property
      //cubes[count] = thingToMake;
      for(var i= 0; i < 8; i++)
      {
          if(board[randomPick-1,i]==null)
          {
              //add the cube to our "game board" to keep track of where it is, this is our 2D array
              board[(randomPick-1),i] = thingToMake;
              break;
         }
      }
      if(board[0,7] != null || board [1,7] != null || board [2,7] != null || board [3,7] != null || board[4,7] != null )
          Application.LoadLevel("LoseScene");
      //halt script for 1 second before returning to the start of the process
      yield WaitForSeconds(1);
      //set spawning back to false so timer may start again
      spawning = false;
      //increment count
      count++;
 }