I deployed a site that was using the AjaxToolKit and had references to the System.Web.Extensions.
I found this error Could not load file or assembly 'System.Web.Extensions, Version=1.0.61025.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35' or one of its depend
This is due that it could not find that assembly System.Web.Extensions or System.Web.Extensions.Design in the bin or the GAC folder C:\Windows\assembly.
I solved this error my installing the ASP.NET AJAX 1.0 package from Microsoft.
You can download it at http://www.microsoft.com/downloads/details.aspx?FamilyID=ca9d90fa-e8c9-42e3-aa19-08e2c027f5d6&displaylang=en
This msi installs in your GAC (C:\Windows\assembly) the correct assemblies System.Web.Extensions version 1.0.61025.0