This isn't a leak. I don't have any direct knowledge. But I have been around the block a few times. It's now widely known that the NSA is breaking most encryption on the Internet. What's not known is how.
We also know that the Flame malware was signed by a rogue Microsoft certificate. That rogue Microsft certificate was hashed with MD5, which is what allowed it to be impersonated.
On my Ubuntu box I just ran an analysis of the Root CA certificates (from the ca-certificates package which itself comes from Mozilla). This certificate list is widely used by thrird-party programs as an authoritative list. But other distributors (e.g., Google, Apple, Microsoft) have a substantially similar list due to the need for SSL to work in all browsers. If any one vendor shipped a substantially different list then end users would merely preceve that browser as being broken and not use it.
Back to my analysis. Mozilla includes 20 Root CA certificates that use MD5 and 2 that use MD2. This is frightening. We already know that a Microsoft certificate with MD5 was used to distribute the Flame malware and it is all but proven that Flame was created and distributed by the U.S. government.
The situation is clear. The NSA is in the posession of one or more Root CA keys. It is only prudent to expect that the NSA has spoofed copies of all 22 CAs that use MD5 or MD2. It is also possible that they have exact copies (i.e., true keys, not spoofed) of other major U.S. based certificate authorities (I shudder to think of a world where a national security letter requests a Root CA key as being relavent to an investigation).
The NSA would then use these keys to spoof SSL certificates in real time, creating Subjects identical to the target web site, becoming a completely invisible man-in-the-middle. This method would be impossible to detect for all but the most skilled users.
Edit: Turns out I was right on the money.
Edit April 2014: Heartbleed notwithstanding, I still firmly believe the NSA is actively executing MITM attacks using genuine or spoofed Root CA keys. Why let an IDS fingerprint you when you can engage in active and undetectable surveillance?