The below code when initialised against a div will easily fade in and fade out a div. The code is simple and well contained. Steps is the number of opacity changes to make to go from 0 opacity to 100. Duration is the time in ms betweeen each step. Low duration and high steps make for a smoother fade but is more taxing on resources.

Also included (coz my code uses it) is an implementation for a javascript version of String.Format (String.format in this case); a wonderful piece of handy functionality.

function fadeManager(div, steps, duration){
 this.div = div;
 this.steps = steps;
 this.duration = duration;
 this.stepCount = 0;
 this.alphaStep = (1 / steps) * 100;
 this.handle = null;
 div.manager = this;
 
 this.fadeIn = function (){
  ref = this;
  this.div.style.filter = String.format("progid:DXImageTransform.Microsoft.Alpha(opacity={0})", this.alphaStep * this.stepCount);
   
  if (this.stepCount == 0)
   this.initialise();
   
  this.stepCount++;
  
  if (this.handle == null)
   this.handle = window.setInterval(function() { ref.fadeIn(); }, this.duration);
   
  if (!(this.stepCount < this.steps)){
   this.reset();
  }
 };
 
 this.fadeOut = function() {
  ref = this;
  opacity = (this.alphaStep * this.stepCount);
  this.div.style.filter = String.format("progid:DXImageTransform.Microsoft.Alpha(opacity={0})", opacity);
   
  this.stepCount--;
  
  if (this.handle == null)
   this.handle = window.setInterval(function() { ref.fadeOut(); }, this.duration);
   
  if (opacity == 0){
   this.reset();
   this.div.style.display = "none";
  }
 }
 
 this.initialise = function(){
  this.div.style.display = "block";
 }
 
 this.reset = function(){
  if (this.handle != null){
   window.clearInterval(this.handle);
   this.handle = null;
  }
 }
}

String.format = function(text){
 if (arguments.length == 0)
  throw "Text argument is required.";
  
 if (arguments.length == 1)
  return text;
 
 formatReg = /\{(\d){1}\}/g;
 formatArgs = arguments;
 
 return text.replace(
   formatReg,
   function(){
    index = parseInt(arguments[1]);
    return formatArgs[index+1];
   }
  )
}

I use this in an app to fade in and out some help text. To open it I call a handy func just for code reuses sake.

function openHelp(id){
 div = document.getElementById(id);
 
 var man = new fadeManager(div, 15, 75);
 man.fadeIn();
}

Enjoy!