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[–] 26556987? ago 

there are excellent open source compiler frameworks like the excellent llvm/clang stack which, for instance, Apple bases its language compilers off of

so one could get a great deal of leverage by just starting with such an existing compiler and the going to the code generation module (a distinct module in llvm) and work on that to obfuscate - even the higher degrees of optimization alone can tend to make the actual machine instruction sequence rather non-obvious relative to the original source code, but with actual intent, a higher degree of obfuscation could be acheived.

Or one could transform ordinary binary instruction code into an encrypted form that has to be decrypted before it can execute on the target CPU. The decryption could be built into a custom page loader - the decryption key could be provided at program execution time and the key might be kept on something like a removable usb stick or smart card