<p>If I'm using Visual Studio 2008 targeted to ASP.NET 2.0, then which version of the Ajax Control Toolkit should I be using?</p>

You need the Toolkit version
1.0.20229.20821
,
AjaxControlToolkit.zip
the dll's are targeted to .NET 2.0 and you need also the
ASP.NET AJAX Extensions 1.0 for .NET 2.0
.