Reading through some of the comments in this thread, I'm coming to the conclusion that a lot of people forgot to take their Thorazine today; I'm not talking about this post in particular, there are others way worse. But there sentiment, based on the same misunderstanding is the same. I'm sure I'm going to get flamed to death for this, but on the off chance that somebody actually finds this informative and helps them think about and discuss the topic in a more informed manner, here goes:
There is no "secret evidence", not the way you're using it. Using this case as an example, what happens is that information is developed (in this case, by the NSA) using sources and methods that the government does not want exposed to the public. So the NSA passes along a lead to the FBI, saying in essence, "You may find it instructive to look at this person's phone records during this time-frame". The FBI then makes requests to do just that, using standard procedures that can safely be talked about in open court, like using court orders and/or subpoenas. In other words, **they reconstruct the information in such a way as to protect the method used initially to identify the suspect/defendant.** The suspect/defendant still sees all of the evidence that is being used against him. So claiming that there is "secret evidence" is uninformed. The only thing secret is initial method used.
For the record, I am in no way trying to justify or defend anything that has come out in the wake of Snowden's disclosure about NSA's domestic surveillance programs. I'm not addressing it one way or the other. I'm strictly referring to the issue of "secret evidence" which seems to have gotten everybody's knickers in a twist.
Disclaimer: I work for a federal law enforcement agency.