http://www.amazon.com/Top-Secret-America-American-Security/d...
This article is from a while back and in the intervening time the journalists came out with a book that goes into more detail.
With compartmentization and the short terms of congress people (2 years and then there could be a change, worse if the party in control switches) nobody knows what our top secret money is spent on. It's so bad that we ask the people we give the money to if what they are doing is worth while because nobody knows and nobody wants to be the guy that cut the budget of x y ad z and let the terrorists attack again.
Think on the order of a half trillion dollars that they can kind of account for (it's black, could be more, probably not tons less) that we have no idea what it actually does.
Funny thing, NSA might not know and probably doesn't have an easy way to find out. This is an artistic response in that it doesn't make them sound like idiots for not knowing. there is just a staggering amount of communication going on, even if tried really hard to follow the rules try would still screw up.
Top Secret America by Dana Priest (http://www.amazon.com/Top-Secret-America-American-Security/d...) is a somewhat interesting read on it. There are some politically angled results you can take from it but one of the most obvious non-political results is that the national security apparatus employs people that tend to be better paid, live in better areas and have all those benefits (better schools for their kids, less crime, etc..) They also seem to be disproportionately white men. If you squint your eyes just right, it looks an awful lot like a jobs program for white men. The book is a few years old but as I remember it I want to say the average pay for a top secret cleared generic 'analyst' was in the $150k+ range, more if you're in a valuable specialty. Then the real kicker, most of them justify their own jobs and contracts, oversight consists of reading that justification, which I guess isn't totally unusual for government work but since they're contractors it's a little odd.. It's not performance based.