Today I was playing a bit with Visual Studio 2008 and was surprised to see that I was not getting IntelliSense in my web.config. As you might already know IntelliSense in Xml in Visual Studio is implemented by using a set of schemas that are stored in a folder inside the VS folder, something like: \Program Files\Microsoft Visual Studio 9.0\Xml\Schemas. After looking to the files it was easy to understand what was going on, turns out I was developing using .NET 2.0 settings and Visual Studio now ships different schemas for Web.config files depending on the settings that you are using: DotNetConfig.xsd, DotNetConfig20.xsd and DotNetConfig30.xsd.
As I imagine I looked into the DotNetConfig.xsd and it indeed has all the definitions for the system.webServer sections as well as the DotNetConfig30.xsd. However, DotNetConfig20.xsd does not include the section details, only its definition, so to fix your IntelliSense you can just open DotNetConfig.xsd, select the entire section from:
<xs:element name="system.webServer" vs:help="configuration/system.webServer">...</xs:element>
and just replace the entry in DotNetConfig20.xsd. You might also want to copy the system.applicationHost section and add it to the DotNetConfig20.xsd since it does not include it as well.