I have seen this question in forums as well as many emails on how to configure two versions of the .NET Framework to work with IIS for different sites. I thought I would share the steps outline below that someone wrote:
Install both versions of the Frameworks on the IIS box.
In this case all the web sites are already running on version 1.143 and we want a new site to work with version 2.0.50727.
Using aspnet_regiis –i; register only one version for the IIS.
Click on Web Service Extensions.
Click on Add a new Web service Extension.
Add the Prompt: Put in a legible name for the extension: e.g.: ASP.NET v2.0.50727
Click on Add for required files.
Select the: aspnet_isapi.dll from the correct directory.
Correct directory as in: C:\WINNT\Microsoft.NET\Framework\v2.0.50727
Since this is the new version that we want to work with for the new site.
Check the box that says: “Set extension status to Allowed”
Click OK and make sure the extension is running.
Next: Select the website / virtual directory that need to be run in the new version of the framework.
Right click and then select Properties.
Go to the Home Directories Tab.
Click on the Configuration button.
On the Mappings Tab: Click Add to add an Application Extension.
Click on Browse to choose the same executable DLL you had chosen earlier for the Web service extension.
Leave the rest of the default selections to be the same.
You are good to go. Test the pages for both the frameworks and they should both work now.