One idea that's just crossed my mind is the idea of serving different Javascript to each client? It could be obfuscated uniquely every time someone loads the page in a detectable way. I,e you can serve IP x.x.x.x with obfuscation seed y and then you know to expect a certain behaviour. Variables and program flow can be changed to confuse nieve would be hackers, but important the structure of the network communication can be changed in a subtle way. Any hack scripts would need to counter for this which would make things far more complicated.
I wish my university term would be over so I can start hacking away on this idea! :)