Out of the box VS 2008 doesn't include project templates for creating brand new ASP.NET 2.0 with ASP.NET AJAX 1.0 applications.  Right before Christmas we shipped a web free web download for VS 2008 that enables these project templates options.  You can download them here (note: you also need to make sure you have ASP.NET AJAX 1.0 installed on your machine in order to use them). 

Once these additional project templates are installed, you can use File->New Project or File->New Web Site within VS 2008 to create ASP.NET AJAX 1.0 applications that run on ASP.NET 2.0:

Figure 1: New ASP.NET AJAX 1.0 Web Site

Figure 2: New ASP.NET AJAX 1.0 Web Application

Applications built using these project templates do not require .NET 3.5 to be installed on a server in order to work - you can copy them to any existing web server that has .NET 2.0 and ASP.NET AJAX 1.0 installed and they will work fine.

Hope this helps,

Scott