At first glance, it should be easy to inject a javascript, but it took a little bit of digging around to figure out the resolution, the key is to use ScriptManager.

   1: <asp:UpdatePanel ID="myUpdatePanel" UpdateMode="Conditional" runat="server">
   2:    <Triggers>
   3:       <asp:AsyncPostBackTrigger ControlID="btnClick" EventName="Click" />
   4:    </Triggers>
   5:    <ContentTemplate>
   6:        <asp:ImageButton 
   7:           ID="btnClick" 
   8:           ImageUrl="ClickMe.png" 
   9:           runat="server"
  10:           CausesValidation="false" 
  11:           OnClick="btnClickEvent"
  12:           ToolTip="Click Me" 
  13:           AlternateText="Click me!" />
  14:    </ContentTemplate>
  15: </asp:UpdatePanel>

We wanted to dynamically inject some JavaScript code. If my ScriptManager control has EnablePartialRendering set to true, it's a simple matter of registering the script. What i didn't realize earlier was that you don't need to the use the current page or current event, you need to call the static method on the ScriptManager class. 

   1: protected void btnClickEvent(object sender, ImageClickEventArgs e)
   2: {
   3:    btnClick.Text = "I was clicked."
   4:    btnClick.Disabled = true;
   5:    ScriptManager.RegisterClientScriptBlock(myUpdatePanel, typeof(UpdatePanel),myUpdatePanel.ClientID, "alert('It worked!');",true);            
   6: }

That's it! Use the ScriptManager class, point it to the instance of your update panel, pass it a unique key and then the JavaScript you want, and it will be executed once the update panel is done rendering.