You can use HTMP Protector.
The only file you will need to protect is your header.php file in your main Nuke directory.
That little program is pretty darn awesome. You can tell it to protect all your images, links etc. You can even disable right clicking and people from viewing your Page source.
It does much more than I can explain.
You can get a trial version here
http://www.antssoft.com/htmlprotector
Pretty darn cool program.
We use it here.
You can even keep users from striking and copying text or anything...You definately need to check it out.