Are MicrosoftAjax.js, MicrosoftMvcAjax.js and MicrosoftMvcValidation.js obsolete as of ASP.NET MVC 3?

Yes, all Microsoft* helpers are obsolete in ASP.NET MVC 3. For me they have always been obsolete but now at least Microsoft made this official and replaced them with jQuery.

2 new functionalities have been introduced

<appSettings>    <add key="webpages:Version" value="1.0.0.0"/>    <add key="ClientValidationEnabled" value="true"/>    <add key="UnobtrusiveJavaScriptEnabled" value="true"/></appSettings>

The first is UnobtrusiveJavaScriptEnabled. This means that if you enable this functionality in your web.config (its enabled by default when you create a new ASP.NET MVC 3 application), all the Ajax.* helpers such as Ajax.BeginForm and Ajax.ActionLink will emit HTML5 data-* attributes on their respective DOM elements instead of mixing javascript with markup. Then you should include the jquery.unobtrusive-ajax.js script to your page which will parse those attributes and use jQuery to unobtrusively AJAXify them.

The second is ClientValidationEnabled which is also enabled by default. The same way unobtrusive javascript works, when you enable this setting all helpers that generate input fields will emit HTML5 data-* attributes on them. Then you include jquery.validate.js and jquery.validate.unobtrusive.js scripts to make them work, such as in your _Layout.cshtml. They must appear in this order, and they must be after jquery is loaded:

<script src="@Url.Content("~/Scripts/jquery-1.7.1.min.js")" type="text/javascript"></script><script src="@Url.Content("~/Scripts/jquery.validate.min.js")" type="text/javascript"></script><script src="@Url.Content("~/Scripts/jquery.validate.unobtrusive.min.js")" type="text/javascript"></script>

So in ASp.NET MVC 3 you can forget about all Microsoft* scripts. Remove them from your site. Delete those files.

You only need the MicrosoftAjax functionality if you are using the libraries. Microsoft AJAX does offer some functionality not found in the provided JQuery libraries (although could be replicated with plug-ins). If you are not using Microsoft AJAX within your application you can delete all reference to these scripts.