If you are doomed to run IIS for whatever reason here is a way to keep it a secret without using ISAPI filters.

Do a dir %windir%\w3svc.dll and note all of the locations where w3svc.dll exists.
Make a directory called foo
Copy w3svc.dll to \foo
Make a backup copy of the original
Fire up your favorite hex editor (Visual C++ works but make sure you open the file as a binary).
Goto offset 004C70
There you will see the string Microsoft-IIS/5.1 (your version may vary)
You can replace this string with any string of the exact same length of ascii characters. Sorry unicode does not work here.
Do not make the new string any longer then the existing one (17 characters on my box).
Pad the string with spaces if you use a shorter string.

Copy your altered w3svc.dll to all of the locations noted above with the %windir%\system32\w3svc.dll being the last copy operation.

have fun!