From the BBC's article on the danish website defacements..:
However, he added, secondary defacements buried within a website can last for months or years before they are found and removed by website administrators.So wait.. You don't run some kind of analysis tool after you notice your b0x has been Pwn3d?? Tripwire comes to mind.. or even just diff or perl??
You do have the stuff to generate your website behind your firewall, don't you?