Bruce Schneier has a few essays on this topic. He tries to work out ways to secure yourself against the NSA, but the real fight is going to be among the Internet engineers.
The impressively bearded Jack Daniel brings up a very interesting question: can you trust NSA employees? How do you really know they’re former NSA employees and not just “former” employees? The problem is that so many eggs are in that one basket: for decades, the NSA has been on the top shelf when it comes to cryptography and other security-related issues, and there are only so many top-notch security people around without any NSA influence, so a big company is really limiting itself if it goes down this route.