This is probably far from the most elegant solution, but its a solution nonetheless:
public class UpdatePanel : System.Web.UI.UpdatePanel
{
    /// <summary>
    /// Javascript to be run when the updatepanel has completed updating
    /// </summary>
    [Description("Javascript to be run when the updatepanel has completed updating"),
        Category("Values"),
        DefaultValue(null),
        Browsable(true)]
    public string OnUpdateCompleteClientScript
    {
        get
        {
            return (string)ViewState["OnUpdateCompleteClientScript"];
        }
        set
        {
            ViewState["OnUpdateCompleteClientScript"] = value;
        }
    }
    protected override void OnPreRender(System.EventArgs e)
    {
        base.OnPreRender(e);
        if(!string.IsNullOrEmpty(this.OnUpdateCompleteClientScript))
            Page.ClientScript.RegisterStartupScript(this.GetType(), this.ClientID, string.Concat("Sys.WebForms.PageRequestManager.getInstance().add_endRequest(function(sender, args){for(var panelId in sender._updatePanelClientIDs){if(sender._updatePanelClientIDs[panelId] == '", this.ClientID, "'){", this.OnUpdateCompleteClientScript, "}}});"), true);
    }
}
Use it like this:
<uc:UpdatePanel OnUpdateCompleteClientScript="alert('update complete');">
    <!-- stuff in here -->
</uc:UpdatePanel>
Of course you'll need to register the custom control in youre webconfig or page to use it like this.
Edit: also, have you looked at jquery.live?