For Windows Server 2003 :

HKEY_LOCAL_MACHINE\ SYSTEM\ CurrentControlSet\ Services\ DNS\ Parameters\ GlobalQueryBlockList
Edit the value as you wish.

For Windows Server 2008 :

• To remove wpad but keep isatap in block list :
  dnscmd /config /globalqueryblocklist isatap
• To remove isatap but keep wpad in block list :
  dnscmd /config /globalquerybloclist wpad