You would need to add the scripts as resources to a seperate library and reference them from there to take advantage of the script combiner.
Edit to provide an walk through
Create a new Class Library project (called for example "CombinedScipts"), remove the default class.
Add a reference to both the AjaxControlToolkit and System.Web
Add your JS files to the project, and change their Build Action property to "Embedded Resource".
Open the AssemblyInfo.cs file
Add the following:
// You need to add a web resource call for each JS file in the project
[assembly: WebResource("CombinedScripts.Console.js", "text/javascript")]
[assembly: WebResource("CombinedScripts.Utilities.js", "text/javascript")]
// Not setting IncludeScripts or ExcludeScripts marks all scripts as
// combinable.
[assembly: AjaxControlToolkit.ScriptCombine()]
Add this library as a reference in your web site project.
In your project, you can then add the following between the ToolkitScriptManager tags:
assembly="CombinedScripts" />
assembly="CombinedScripts" />
Not forgetting to ensure that the CombineScripts property of the ToolkitScriptManager is set to true.
This then results in one call to something like:
/pageName.aspx?_TSM_HiddenField_=ToolkitScriptManager1_HiddenField&[...]
Which will have your combined scripts in, with comment delimiters like:
//START CombinedScripts.Console.js
[...]
//END CombinedScripts.Console.js
//START CombinedScripts.Utilities.js
[...]
//END CombinedScripts.Utilities.js