I've reformated a CF card that the camera couldn't us anymore using fdisk under Linux to rewrite the partition table.
I recently tried to do the same thing for a CF card my Sister had corrupted using her XP laptop and I failed to convince XP to re-write the partition table....
A CF card is 'just another disk' to the computer, so for CF cards at least any tool you would use on a hard disk should help with a CF card.