Some people have suggested code that does things like encrypt some critical parts of the code and decode them on the fly at runtime, using a key that's generated by checksumming the file and XORing with the last 8 bytes or some variant.
The neatest trick I heard of was to use the 68000's single step mode to decrypt each word of the program on the fly, run it, then write it back reencrypted under another key, so that a decrypted copy never existed in memory, and what was there was a moving target. Unfortunately, the decrypting software did sit in memory, and so you could eventually hack that right out, and decode the core image.
I've heard people talk about doing totally encrypted computation, but I'm not sure whether anything practical hs been implemented.
There was a CMU (I think) paper on the subject, but it assumed fully protected hardware (CPU's wrapped in huge quantities of wire all sealed in epoxy etc.) Such hardware tricks - as I think the NSA learned with ViaLink - are never completely satisfactory. :) Ian.