What is the difference between ASP.Net AJAX ScriptManager and Ajax control ToolkitScriptManager?

Both the script manager differ in the way they render the javascript behaviour files to the client side. ToolkitScriptManager uses a technique called script combining to download the scripts and improves the performance.

Recomended reading,
http://blogs.msdn.com/delay/archive/2007/06/11/script-combining-made-easy-overview-of-the-ajax-control-toolkit-s-toolkitscriptmanager.aspx