One of the fascinating things about working in the nation's capitol was/is seeing how reality differs from the textbooks. In theory, Congress passes laws "authorizing" expenditure of money and separate yearly appropriations acts specifying the amount of money that can be spent for authorized purposes. In theory, the Constitution provides for a system of checks and balances among the three branches of government. In reality Congress is an example of the evolution of fungus. It turns out that trees depend on fungi, that each tree has an associated type of fungus--the fungus helps to extract nutrients from the soil.
I call Congress a fungus because its influence is underground and unnoticed. Take the 2006 Agriculture Appropriations Act just passed by the House. (Go to http://thomas.loc.gov and search for it.)
The bulk of the act consists of appropriations in the classic sense, but Title VII includes the fungal growths. Here are contained the specific "dos and don'ts" that pass beneath the notice of the media. These may originate as requests from a member's district or State, or they may represent a bee in someone's bonnet. I'm not 100 percent sure of how they actually get into the bill--I suspect there's little or no discussion in the committee. Each member has her or his own priorities and goes along with those of others. I think it's possible for some to raise a point of order when the bill is considered--you aren't supposed to legislate in appropriations acts--but if everyone goes along they get on through.
Some of these provisions do get scrutiny, mostly the ones that represent Congressional "pork". But those that prohibit spending are almost never mentioned.