I wonder why the common assumption is that the NSA doesn't run Tor nodes. Why wouldn't they?
The NSA's (authorized) budget is $10.8 billion[1]. For $5 you can get a server with 20GB SSD and 1TB of transfer per month. It doesn't seem like it'd take very much money to be able to ensure that at least, say, 1% of Tor users' traffic passes through your entry and exit nodes, de-anonymizing them. So over a long enough time scale, that would de-anonymize quite a lot of interesting traffic, and interesting users.
One solution is VPN over Tor. But the NSA claims they've cracked 30 VPN providers, and are focused on cracking the rest as soon as possible. That's a lot of compromised VPN providers.
You could set up your own server and use that as a VPN, but if you pay with Bitcoin, then it's trivial to analyze the blockchain to tie your identity to the server, unless you use a tumbling service like bitcoinfog. But even if you manage to get a server set up anonymously, then what? You still would want to use VPN over Tor, since that's your best bet for privacy. But as soon as you get de-anonymized on Tor, that correlates your home IP address with your anonymous server, thus de-anonymizing your server too.
I can't think of any options to be truly safe from a global passive adversary that doesn't also cost >1MM to set up initially. Any ideas?
[1] http://www.washingtonpost.com/wp-srv/special/national/black-...