The existing answers are now outdated. The getBoundingClientRect() method has been around for quite a while now, and does exactly what this question asks for. Plus it is supported across all browsers.

From this MDN page:

The returned value is a TextRectangle object, which contains read-only left, top, right and bottom properties describing the border-box, in pixels, with the top-left relative to the top-left of the viewport.

You use it like so:

var viewportOffset = el.getBoundingClientRect();
// these are relative to the viewport
var top = viewportOffset.top;
var left = viewportOffset.left;

//First get the correct geometry for the browser

(function(){
 Run= window.Run || {};
 if(window.pageYOffset!= undefined){
  Run.topLeftScroll= function(hoo){
   var wo= [window.pageXOffset, window.pageYOffset]
   if(hoo && hoo.nodeType== 1){
    hoo= mr(hoo);
    var T= 0, L= 0;
    while(hoo){
     L+= hoo.offsetLeft;
     T+= hoo.offsetTop;
     hoo= hoo.offsetParent;
    }
    wo= [L, T, wo[0], wo[1]];
   }
   return wo;
  }
 }
 else if(document.body.scrollTop!== undefined){
  Run.topLeftScroll= function(hoo){
   var B= document.body;
   var D= document.documentElement;
   D= (D.clientHeight)? D: B;
   wo= [D.scrollLeft, D.scrollTop];
   if(hoo && hoo.nodeType== 1){
    hoo= mr(hoo);
    var T= 0, L= 0;
    while(hoo){
     L+= hoo.offsetLeft;
     T+= hoo.offsetTop;
     hoo= hoo.offsetParent;
    }
    wo= [L, T, wo[0], wo[1]];
   }
   return wo;
  }
 }
})()

// shortcut function

if(window.Run && Run.topLeftScroll){
 Run.getPosition= function(who, wch){
  var A= Run.topLeftScroll(who);
  if(!wch) return A;
  switch(wch.toUpperCase()){
   case  X : return A[0];// element Left in document
   case  Y : return A[1];// element Top in document
   case  L : return A[0]-A[2];// Left minus scroll
   case  T : return A[1]-A[3];// Top minus scroll
   case  SL : return A[2];// scroll Left
   case  ST : return A[3];// scroll Top
   default: return 0;
  }
  // all returns are integers (pixels)
 }
}

Check out what the JS Frameworks have to offer. Mostly, they have worked out all - or at least most - of the browser specific problems and specialties.

In Prototype, there are the scrollOffset() functions. I m not familiar enough with JQuery to point you to the right manual page but here is a question that seems to go towards the right direction.

I ve shearshed a little bit and found this :

 function getOffsetPosition(el_id, side){
 element = document.getElementById(el_id);

 newNode = document.createElement("div");
 newNode.innerHTML = "<div style="height: 12px;"></div>";
 element.insertBefore(newNode, element.firstChild);

 iVal = 0;
 oObj = element;
 var sType = "oObj.offset"+side;
 while (oObj && oObj.tagName != "html") {
 iVal += eval(sType);
 oObj = oObj.offsetParent;
 }
 element.removeChild(newNode);
 return iVal;
 } 

If that can help you ^^