When deleting a file at work from a HDD what is the best way to ensure that the file cannot be recovered? ie that the data no longer exists on the drive, rather than just resetting the flag of the relevant file/cluster? Is there any way NTFS will do this? Registry hacks etc?

There are no standard mechanisms for this. Please use third party privacy software (such as Disk Wiper feature in ZDelete) to eliminate unused MFT entries and overwrite clusters containing deleted data.