It took me some time to find out, what options I had to enable to enable debugging in a Whidbey ASP.Net project in windows 2003 server, so maybe this is usefull for someone.

Start with a regular webproject, using the IIS Manager map a virtual directory (EKPool in this picture) to the directory where you created this webproject. Make sure it's an application on the "Directory"-tab and make sure it's using v 2.0.* of the framework on the "ASP.Net"-tab.

Allow the "ASP.NET v2.0.*" Web Service Extension, prohibited by default.

Open the "property pages" of your webproject. Change the Server property on the "Start Options"-tab to "Use custom server" and enter the path to the virtual directory you just created in the "Base Url" textbox. Check the ASP.NET debugging checkbox.

Check the web.config file for the "compilation node" :<compilation debug="true" defaultLanguage="c#" />.

Start debugging with [F5] or run the application without debugging with [CTRL]+[F5].

This also works if you create an application in the root of your website, something which won't work, when you use the integrated webserver in Visual Studio Whidbey.