I came across this error when i was trying to ajaxify my sharepoint site.
After adding the AjaxifyMoss from the codeplex developed by Richard Finn.
And tried loading my site i got the error
Error: The base type 'System.Web.UI.MasterPage' is not allowed for this page
So i decided to check the web.config and i noticed the SafeControl tag doesn't have the .Net 2.0 assembly included despite the fact i added both vsersios 2.0 and 3.5.
Its possible the.Net 3.5 assebply overwrote the 2.0.
Anyway after i added the below which is the 2.0 verison
<SafeControl Assembly="System.Web, Version=2.0.0.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a" Namespace="System.Web.UI" TypeName="*" Safe="True" AllowRemoteDesigner="True" />
And refreshed my page. It worked 