<p>So I have this app that checks for updates on the server getting a JSON response, each new update is put at the top of my list on a new div that is added via insertBefore using javascript.</p>

<p>All works just fine, but i'd like to add an animation effect when the div is added, i.e. "slowly" move the existing divs down, and add the new one at the top, Any pointers on how to do that ?</p>

<p>The application actually runs in facebook not using the iframe, I tried to use jquery but it does not seem to work on facebook, and looking at the code modifications that FB do, I assume other frameworks will have a similar problem.</p>

It depends on the JavaScript framework you're using; but look at
MooTools
,
Scriptaculous
,
jQuery
and
YUI Animation
. If you're just hammering out JavaScript on your own, you'll find that working with interval timers that modify the style of some element over time and then trigger an animation complete event to stop the timer and finally update the page is a fairly involved error prone process.
You're probably looking for something generally called
slide
down
(try the demos).