While poking at a recent project with a large stick my script resource handler began coughing and gave me a nasty timeout error. After a little prodding of google I came up with this fix. It works, assuming you don't actually have something wrong with your code that is timing out.
In your master page or page where your script manager lives add the AsyncPostBackTimeout value. The default is 90 seconds in case you're wondering.
<asp:ScriptManager ID="ScriptManager1" runat="server" AsyncPostBackTimeout ="360000"></asp:ScriptManager>
In your web.config file, add this to your system.web section.
<httpRuntime executionTimeout="360000"/>
That's it. Your pages shouldn't timeout now unless you've broken something else. :)