After upgrading Windows Server 2003 to framework 3.5 and publishing some project to IIS6 , with files with extensions .wsdl , when we tried to browse the file from Published Virtual Directory in IIS we got 404 .
The solution was to enter to the properties of the project -> Virtual Directory (Home Directory) -> Configuration -> Find .wsdl extension -> Remove.

Another possible solution is to enter
Web Service Extensions -> Add a new Web Service Extention ->
add SOAPIS30.dll -> Allow

The second solution is not checked,because the first one worked for us , but you can try it.