Defense Secretary Donald Rumsfeld leaked that the military had over $2 trillion unaccounted for in the budget. That seems like it is a large mistake, or Mr Rumsfeld may have said something that wasn't supposed to be made public.
Not only do they have dummy projects that help fund some of the black budget, but they also own many companies where they use the profits to help with funding.
There is no way to account for what actually is in these budgets as the ones that Congress deals with are classified, and other monies are hidden.
TV shows are fantasy and made up. The black budget programs are very real.