Resetting NTFS Permissions Disk Wide

If you're talking about a disk that doesn't contain a Windows installation, just use the "TAKEOWN" and "ICACLS" utilities:

TAKEOWN /f "X:\" /r /d y
ICACLS "X:\" /reset /T

Then you can reset the ACLs to whatever you want.

If it's a disk with a Windows 2000, XP, or Server 2003 operating system installed (don't know about Vista on this one) you could try re-applying the default security template:

secedit /configure /db secedit.sdb /cfg %SystemRoot%\defltwk.inf /overwrite /verbose

(On a Windows Server install, substitute "defltsv.inf" for "defltwk.inf".)

As an alternative to takeown and *cacls you can use SetACL to first take ownership of every file and directory on the drive and then set the desired permissions.

Setting the owner of an entire tree to administrators and enabling inheritance on the child objects:

SetACL.exe -on "C:\" -ot file -actn setprot -op "dacl:np;sacl:nc" 
           -rec cont_obj -actn setowner -ownr "n:S-1-5-32-544;s:y"

Adding full permissions for administrators:

SetACL.exe -on "C:\" -ot file -actn ace -ace "n:S-1-5-32-544;s:y;p:full"