Recently I had to move an internal CA from one server to another. That process in itself was a real pain, but after the move and reinstall of the cert services I had forgotten to install IIS so the cert installer did not give me the virtual directories for the web enrollment.
I figured i would have to create the vdirs manually but then i checked the certutil.exe utility first to see if there was anything in the help screen about vdirs.
Holy smokes, there is, its a –vroot paramater adding this to the certutil.ee command will automagically create you vdirs for you. SWEET!
If you need to recreate you certificate server virtual directories just run the following command and you will now have them in IIS
certutil.exe –vroot
out!