This really doesn't have to be too difficult. Put 1000 XMR aside for anybody that can break Monero's cryptography. Has to be validated by Shen. Or 1000 XMR for anybody that can expose a network-breaking bug. Has to be validated by Moneromooo. Surely those two individuals have put so much time into this coin that they would be interested to hear from anybody who claims they've figured out a major exploit.
If they're worried about getting 100s of spam emails a day claiming the bounty, perhaps set up a middleman to delete all the crap emails and only forward on those that seem to hold promise.
Others have said, with some validity, that a real profit incentivized hacker wouldn't care about a 1000 XMR bounty, but would simply short XMR and then run the exploit. But I think the bounty would encourage those who are part of the community, yet possess some hacking skills, to put their talents to good use, and thus help the community while still getting "paid" for their time.